SWISS-MODEL Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "Papain-like protease nsp3 | P0DTD1 PRO_0000449621" submitted to SWISS-MODEL workspace on May 5, 2023, 9:33 p.m..The submitted primary amino acid sequence is given in Table T1.

If you use any results in your research, please cite the relevant publications:

Results

The SWISS-MODEL template library (SMTL version 2023-05-05, PDB release 2023-04-28) was searched with for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 1456 templates were found (Table T2).

Models

The following models were built (see Materials and Methods "Model Building"):

Model #02

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer (matching prediction)
1 x ZN: ZINC ION;
0.14 0.80 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
6w9c.1.A 100.00 homo-trimer 0.26 HHblits X-ray 2.70Å 0.63 748 - 1060 0.16 Non-structural protein 3

Included Ligands

Ligand Description
1 x ZN
ZINC ION

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
CL.2 Not biologically relevant.
CHLORIDE ION
CL.4 Not biologically relevant.
CHLORIDE ION
CL.7 Not biologically relevant.
CHLORIDE ION
ZN.3 Binding site not conserved.
ZINC ION
ZN.5 Binding site not conserved.
ZINC ION
ZN.6 Binding site not conserved.
ZINC ION

Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
6w9c.1.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
6w9c.1.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
6w9c.1.A --------------------------------------------------------------------------------

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
6w9c.1.A --------------------------------------------------------------------------------

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
6w9c.1.A --------------------------------------------------------------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
6w9c.1.A --------------------------------------------------------------------------------

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
6w9c.1.A --------------------------------------------------------------------------------

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
6w9c.1.A --------------------------------------------------------------------------------

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
6w9c.1.A --------------------------------------------------------------------------------

Target SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF
6w9c.1.A -------------------------EVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF

Target YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA
6w9c.1.A YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA

Target YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
6w9c.1.A YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ

Target FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE
6w9c.1.A FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE

Target YKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFA
6w9c.1.A YKGPITDVFYKENSYTTTIK------------------------------------------------------------

Target DDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
6w9c.1.A --------------------------------------------------------------------------------

Target VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAA
6w9c.1.A --------------------------------------------------------------------------------

Target YVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQ
6w9c.1.A --------------------------------------------------------------------------------

Target LCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
6w9c.1.A --------------------------------------------------------------------------------

Target MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFF
6w9c.1.A --------------------------------------------------------------------------------

Target YVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA
6w9c.1.A --------------------------------------------------------------------------------

Target TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
6w9c.1.A --------------------------------------------------------------------------------

Target GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVS
6w9c.1.A --------------------------------------------------------------------------------

Target DVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLS
6w9c.1.A --------------------------------------------------------------------------------

Target HQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
6w9c.1.A --------------------------------------------------------------------------------

Target PFKLTCATTRQVVNVVTTKIALKGG
6w9c.1.A -------------------------




Model #07

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
1 x ACE-UB4-DPP-GLY-GVE: VIR250;
1 x ZN: ZINC ION;
0.14 0.79 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
6wuu.2.A 99.69 monomer 0.00 BLAST X-ray 2.79Å 0.62 744 - 1061 0.16 Non-structural protein 3

Included Ligands

Ligand Description
1 x ACE-UB4-DPP-GLY-GVE
VIR250
1 x ZN
ZINC ION

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
MG.3 Not in contact with model.
MAGNESIUM ION

Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
6wuu.2.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
6wuu.2.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
6wuu.2.A --------------------------------------------------------------------------------

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
6wuu.2.A --------------------------------------------------------------------------------

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
6wuu.2.A --------------------------------------------------------------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
6wuu.2.A --------------------------------------------------------------------------------

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
6wuu.2.A --------------------------------------------------------------------------------

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
6wuu.2.A --------------------------------------------------------------------------------

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
6wuu.2.A --------------------------------------------------------------------------------

Target SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF
6wuu.2.A -----------------------MREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF

Target YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA
6wuu.2.A YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA

Target YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
6wuu.2.A YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ

Target FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE
6wuu.2.A FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE

Target YKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFA
6wuu.2.A YKGPITDVFYKENSYTTTIKP-----------------------------------------------------------

Target DDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
6wuu.2.A --------------------------------------------------------------------------------

Target VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAA
6wuu.2.A --------------------------------------------------------------------------------

Target YVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQ
6wuu.2.A --------------------------------------------------------------------------------

Target LCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
6wuu.2.A --------------------------------------------------------------------------------

Target MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFF
6wuu.2.A --------------------------------------------------------------------------------

Target YVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA
6wuu.2.A --------------------------------------------------------------------------------

Target TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
6wuu.2.A --------------------------------------------------------------------------------

Target GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVS
6wuu.2.A --------------------------------------------------------------------------------

Target DVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLS
6wuu.2.A --------------------------------------------------------------------------------

Target HQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
6wuu.2.A --------------------------------------------------------------------------------

Target PFKLTCATTRQVVNVVTTKIALKGG
6wuu.2.A -------------------------




Model #10

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
1 x TTT: 5-AMINO-2-METHYL-N-[(1R)-1-NAPHTHALEN-1-YLETHYL]BENZAMIDE;
1 x ZN: ZINC ION;
0.14 0.79 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
3e9s.1.A 82.86 monomer 0.00 HHblits X-ray 2.50Å 0.57 746 - 1059 0.16 Non-structural protein 3

Included Ligands

Ligand Description
1 x TTT
5-AMINO-2-METHYL-N-[(1R)-1-NAPHTHALEN-1-YLETHYL]BENZAMIDE
1 x ZN
ZINC ION

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
CL.3 Not biologically relevant.
CHLORIDE ION
CL.4 Not biologically relevant.
CHLORIDE ION

Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
3e9s.1.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
3e9s.1.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
3e9s.1.A --------------------------------------------------------------------------------

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
3e9s.1.A --------------------------------------------------------------------------------

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
3e9s.1.A --------------------------------------------------------------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
3e9s.1.A --------------------------------------------------------------------------------

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
3e9s.1.A --------------------------------------------------------------------------------

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
3e9s.1.A --------------------------------------------------------------------------------

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
3e9s.1.A --------------------------------------------------------------------------------

Target SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF
3e9s.1.A -------------------------EVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTF

Target YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA
3e9s.1.A FVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLALQQLEVKFNAPALQEA

Target YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
3e9s.1.A YYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDN

Target FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE
3e9s.1.A LKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSE

Target YKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFA
3e9s.1.A YKGPVTDVFYKETSYTTTIK------------------------------------------------------------

Target DDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
3e9s.1.A --------------------------------------------------------------------------------

Target VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAA
3e9s.1.A --------------------------------------------------------------------------------

Target YVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQ
3e9s.1.A --------------------------------------------------------------------------------

Target LCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
3e9s.1.A --------------------------------------------------------------------------------

Target MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFF
3e9s.1.A --------------------------------------------------------------------------------

Target YVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA
3e9s.1.A --------------------------------------------------------------------------------

Target TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
3e9s.1.A --------------------------------------------------------------------------------

Target GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVS
3e9s.1.A --------------------------------------------------------------------------------

Target DVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLS
3e9s.1.A --------------------------------------------------------------------------------

Target HQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
3e9s.1.A --------------------------------------------------------------------------------

Target PFKLTCATTRQVVNVVTTKIALKGG
3e9s.1.A -------------------------




Model #01

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
1 x TTT: 5-AMINO-2-METHYL-N-[(1R)-1-NAPHTHALEN-1-YLETHYL]BENZAMIDE;
1 x ZN: ZINC ION;
0.14 0.79 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
3e9s.1.A 82.86 monomer 0.00 BLAST X-ray 2.50Å 0.57 746 - 1059 0.16 Non-structural protein 3

Included Ligands

Ligand Description
1 x TTT
5-AMINO-2-METHYL-N-[(1R)-1-NAPHTHALEN-1-YLETHYL]BENZAMIDE
1 x ZN
ZINC ION

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
CL.3 Not biologically relevant.
CHLORIDE ION
CL.4 Not biologically relevant.
CHLORIDE ION

Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
3e9s.1.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
3e9s.1.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
3e9s.1.A --------------------------------------------------------------------------------

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
3e9s.1.A --------------------------------------------------------------------------------

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
3e9s.1.A --------------------------------------------------------------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
3e9s.1.A --------------------------------------------------------------------------------

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
3e9s.1.A --------------------------------------------------------------------------------

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
3e9s.1.A --------------------------------------------------------------------------------

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
3e9s.1.A --------------------------------------------------------------------------------

Target SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF
3e9s.1.A -------------------------EVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTF

Target YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA
3e9s.1.A FVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLALQQLEVKFNAPALQEA

Target YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
3e9s.1.A YYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDN

Target FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE
3e9s.1.A LKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSE

Target YKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFA
3e9s.1.A YKGPVTDVFYKETSYTTTIK------------------------------------------------------------

Target DDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
3e9s.1.A --------------------------------------------------------------------------------

Target VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAA
3e9s.1.A --------------------------------------------------------------------------------

Target YVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQ
3e9s.1.A --------------------------------------------------------------------------------

Target LCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
3e9s.1.A --------------------------------------------------------------------------------

Target MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFF
3e9s.1.A --------------------------------------------------------------------------------

Target YVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA
3e9s.1.A --------------------------------------------------------------------------------

Target TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
3e9s.1.A --------------------------------------------------------------------------------

Target GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVS
3e9s.1.A --------------------------------------------------------------------------------

Target DVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLS
3e9s.1.A --------------------------------------------------------------------------------

Target HQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
3e9s.1.A --------------------------------------------------------------------------------

Target PFKLTCATTRQVVNVVTTKIALKGG
3e9s.1.A -------------------------




Model #09

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
1 x TTT: 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide;
1 x ZN: ZINC ION;
0.14 0.79 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
7cmd.4.A 100.00 monomer 0.00 HHblits X-ray 2.59Å 0.63 746 - 1060 0.16 Non-structural protein 3

Included Ligands

Ligand Description
1 x TTT
5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide
1 x ZN
ZINC ION

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
ZN.3 Not in contact with model.
ZINC ION

Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
7cmd.4.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
7cmd.4.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
7cmd.4.A --------------------------------------------------------------------------------

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
7cmd.4.A --------------------------------------------------------------------------------

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
7cmd.4.A --------------------------------------------------------------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
7cmd.4.A --------------------------------------------------------------------------------

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
7cmd.4.A --------------------------------------------------------------------------------

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
7cmd.4.A --------------------------------------------------------------------------------

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
7cmd.4.A --------------------------------------------------------------------------------

Target SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF
7cmd.4.A -------------------------EVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF

Target YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA
7cmd.4.A YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA

Target YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
7cmd.4.A YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ

Target FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE
7cmd.4.A FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE

Target YKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFA
7cmd.4.A YKGPITDVFYKENSYTTTIKPVT---------------------------------------------------------

Target DDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
7cmd.4.A --------------------------------------------------------------------------------

Target VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAA
7cmd.4.A --------------------------------------------------------------------------------

Target YVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQ
7cmd.4.A --------------------------------------------------------------------------------

Target LCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
7cmd.4.A --------------------------------------------------------------------------------

Target MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFF
7cmd.4.A --------------------------------------------------------------------------------

Target YVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA
7cmd.4.A --------------------------------------------------------------------------------

Target TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
7cmd.4.A --------------------------------------------------------------------------------

Target GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVS
7cmd.4.A --------------------------------------------------------------------------------

Target DVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLS
7cmd.4.A --------------------------------------------------------------------------------

Target HQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
7cmd.4.A --------------------------------------------------------------------------------

Target PFKLTCATTRQVVNVVTTKIALKGG
7cmd.4.A -------------------------




Model #08

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer (matching prediction)
None
0.13 0.79 ± 0.05
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
2w2g.1.A 75.00 homo-dimer 0.21 BLAST X-ray 2.22Å 0.53 413 - 676 0.14 NON-STRUCTURAL PROTEIN 3

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
SO4.1 Not biologically relevant.
SULFATE ION
SO4.2 Not biologically relevant.
SULFATE ION

Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
2w2g.1.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
2w2g.1.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
2w2g.1.A --------------------------------------------------------------------------------

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
2w2g.1.A --------------------------------------------------------------------------------

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
2w2g.1.A --------------------------------------------------------------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
2w2g.1.A ------------KIKACIDEVTTTLEETKFLTNKLLLFADINGKLYHDSQNMLRGEDMSFLEKDAPYMVGDVITSGDITC

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
2w2g.1.A VVIPSKKAGGTTEMLSRALKKVPVDEYITTYPGQGCAGYTLEEAKTALKKCKSAFYVLPSEAPNAKEEILGTVSWNLREM

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
2w2g.1.A LAHAEETRKLMPICMDVRAIMATIQRKYKGIKIQEGIVDYGVRFFFYTSKEPVASIITKLNSLNEPLVTMPIGYVTHGFN

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
2w2g.1.A LEEAARCMRSLRAPAVVSVSSPDAVTTYNGYLTSSS--------------------------------------------

Target SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF
2w2g.1.A --------------------------------------------------------------------------------

Target YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA
2w2g.1.A --------------------------------------------------------------------------------

Target YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
2w2g.1.A --------------------------------------------------------------------------------

Target FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE
2w2g.1.A --------------------------------------------------------------------------------

Target YKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFA
2w2g.1.A --------------------------------------------------------------------------------

Target DDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
2w2g.1.A --------------------------------------------------------------------------------

Target VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAA
2w2g.1.A --------------------------------------------------------------------------------

Target YVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQ
2w2g.1.A --------------------------------------------------------------------------------

Target LCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
2w2g.1.A --------------------------------------------------------------------------------

Target MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFF
2w2g.1.A --------------------------------------------------------------------------------

Target YVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA
2w2g.1.A --------------------------------------------------------------------------------

Target TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
2w2g.1.A --------------------------------------------------------------------------------

Target GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVS
2w2g.1.A --------------------------------------------------------------------------------

Target DVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLS
2w2g.1.A --------------------------------------------------------------------------------

Target HQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
2w2g.1.A --------------------------------------------------------------------------------

Target PFKLTCATTRQVVNVVTTKIALKGG
2w2g.1.A -------------------------




Model #05

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
None
0.09 0.84 ± 0.07
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
6ywk.3.A 100.00 monomer 0.00 BLAST X-ray 2.20Å 0.61 207 - 376 0.09 NSP3 macrodomain

Excluded ligands

Ligand Name.Number Reason for Exclusion Description
EDO.3 Not biologically relevant.
1,2-ETHANEDIOL
EDO.4 Not biologically relevant.
1,2-ETHANEDIOL
EDO.5 Not biologically relevant.
1,2-ETHANEDIOL
EDO.6 Not biologically relevant.
1,2-ETHANEDIOL
EDO.7 Not biologically relevant.
1,2-ETHANEDIOL
EDO.8 Not biologically relevant.
1,2-ETHANEDIOL
EPE.2 Not biologically relevant.
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
MG.1 Binding site not conserved.
MAGNESIUM ION

Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
6ywk.3.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
6ywk.3.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
6ywk.3.A ----------------------------------------------VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
6ywk.3.A NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
6ywk.3.A NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMK------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
6ywk.3.A --------------------------------------------------------------------------------

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
6ywk.3.A --------------------------------------------------------------------------------

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
6ywk.3.A --------------------------------------------------------------------------------

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
6ywk.3.A --------------------------------------------------------------------------------

Target SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF
6ywk.3.A --------------------------------------------------------------------------------

Target YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA
6ywk.3.A --------------------------------------------------------------------------------

Target YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
6ywk.3.A --------------------------------------------------------------------------------

Target FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE
6ywk.3.A --------------------------------------------------------------------------------

Target YKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFA
6ywk.3.A --------------------------------------------------------------------------------

Target DDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
6ywk.3.A --------------------------------------------------------------------------------

Target VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAA
6ywk.3.A --------------------------------------------------------------------------------

Target YVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQ
6ywk.3.A --------------------------------------------------------------------------------

Target LCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
6ywk.3.A --------------------------------------------------------------------------------

Target MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFF
6ywk.3.A --------------------------------------------------------------------------------

Target YVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA
6ywk.3.A --------------------------------------------------------------------------------

Target TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
6ywk.3.A --------------------------------------------------------------------------------

Target GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVS
6ywk.3.A --------------------------------------------------------------------------------

Target DVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLS
6ywk.3.A --------------------------------------------------------------------------------

Target HQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
6ywk.3.A --------------------------------------------------------------------------------

Target PFKLTCATTRQVVNVVTTKIALKGG
6ywk.3.A -------------------------




Model #06

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
None
0.07 0.75 ± 0.07
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
2kqv.1.A 78.13 monomer 0.00 HHblits NMR - 0.55 551 - 675 0.10 Non-structural protein 3

The template contained no ligands.


Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
2kqv.1.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
2kqv.1.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
2kqv.1.A --------------------------------------------------------------------------------

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
2kqv.1.A --------------------------------------------------------------------------------

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
2kqv.1.A --------------------------------------------------------------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
2kqv.1.A --------------------------------------------------------------------------------

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
2kqv.1.A ----------------------------------------------------------------------GTVSWNLREM

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
2kqv.1.A LAHAEETRKLMPICMDVRAIMATIQRKYKGIKIQEGIVDYGVRFFFYTSKEPVASIITKLNSLNEPLVTMPIGYVTHGFN

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
2kqv.1.A LEEAARCMRSLKAPAVVSVSSPDAVTTYNGYLTSSSKTSEEHFVETVSLAGSYRDWSYSGQRTELGVEFLKRGDKIVYHT

Target SNP-TTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKT
2kqv.1.A LESPVEFHLDGEVLSLDKLKSLL---------------------------------------------------------

Target FYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQD
2kqv.1.A --------------------------------------------------------------------------------

Target AYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYE
2kqv.1.A --------------------------------------------------------------------------------

Target QFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSS
2kqv.1.A --------------------------------------------------------------------------------

Target EYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKF
2kqv.1.A --------------------------------------------------------------------------------

Target ADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTK
2kqv.1.A --------------------------------------------------------------------------------

Target PVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMA
2kqv.1.A --------------------------------------------------------------------------------

Target AYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLL
2kqv.1.A --------------------------------------------------------------------------------

Target QLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNL
2kqv.1.A --------------------------------------------------------------------------------

Target GMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRF
2kqv.1.A --------------------------------------------------------------------------------

Target FYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNR
2kqv.1.A --------------------------------------------------------------------------------

Target ATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVK
2kqv.1.A --------------------------------------------------------------------------------

Target NGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALV
2kqv.1.A --------------------------------------------------------------------------------

Target SDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKL
2kqv.1.A --------------------------------------------------------------------------------

Target SHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNN
2kqv.1.A --------------------------------------------------------------------------------

Target LPFKLTCATTRQVVNVVTTKIALKGG
2kqv.1.A --------------------------




Model #04

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
None
0.05 0.69 ± 0.08
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
2k87.1.A 81.74 monomer 0.00 BLAST NMR - 0.58 1089 - 1203 0.06 Non-structural protein 3 of Replicase polyprotein 1a

The template contained no ligands.


Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
2k87.1.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
2k87.1.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
2k87.1.A --------------------------------------------------------------------------------

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
2k87.1.A --------------------------------------------------------------------------------

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
2k87.1.A --------------------------------------------------------------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
2k87.1.A --------------------------------------------------------------------------------

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
2k87.1.A --------------------------------------------------------------------------------

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
2k87.1.A --------------------------------------------------------------------------------

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
2k87.1.A --------------------------------------------------------------------------------

Target SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF
2k87.1.A --------------------------------------------------------------------------------

Target YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDA
2k87.1.A --------------------------------------------------------------------------------

Target YYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
2k87.1.A --------------------------------------------------------------------------------

Target FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSE
2k87.1.A --------------------------------------------------------------------------------

Target YKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFA
2k87.1.A ------------------------------------------------YTEQPIDLVPTQPLPNASFDNFKLTCSNTKFA

Target DDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
2k87.1.A DDLNQMTGFTKPASRELSVTFFPDLNGDVVAIDYRHYSASFKKGAKLLHKPIVWHINQATTKTTFKPNTWCLRCLWSTKP

Target VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAA
2k87.1.A VDT-----------------------------------------------------------------------------

Target YVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQ
2k87.1.A --------------------------------------------------------------------------------

Target LCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
2k87.1.A --------------------------------------------------------------------------------

Target MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFF
2k87.1.A --------------------------------------------------------------------------------

Target YVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA
2k87.1.A --------------------------------------------------------------------------------

Target TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
2k87.1.A --------------------------------------------------------------------------------

Target GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVS
2k87.1.A --------------------------------------------------------------------------------

Target DVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLS
2k87.1.A --------------------------------------------------------------------------------

Target HQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
2k87.1.A --------------------------------------------------------------------------------

Target PFKLTCATTRQVVNVVTTKIALKGG
2k87.1.A -------------------------




Model #03

File Built with Oligo-State Ligands GMQE QMEANDisCo Global
PDB ProMod3 3.3.0 monomer
None
0.05 0.71 ± 0.11
Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Range Coverage Description
2kqw.1.A 80.22 monomer 0.00 BLAST NMR - 0.55 678 - 732 0.09 Non-structural protein 3

The template contained no ligands.


Target    APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLD
2kqw.1.A --------------------------------------------------------------------------------

Target EWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEED
2kqw.1.A --------------------------------------------------------------------------------

Target WLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
2kqw.1.A --------------------------------------------------------------------------------

Target NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENF
2kqw.1.A --------------------------------------------------------------------------------

Target NQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
2kqw.1.A --------------------------------------------------------------------------------

Target KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
2kqw.1.A --------------------------------------------------------------------------------

Target VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM
2kqw.1.A ----------------------------------------------------------------------GTVSWNLREM

Target LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLN
2kqw.1.A LAHAEETRKLMPICMDVRAIMATIQRKYKGIKIQEGIVDYGVRFFFYTSKEPVASIITKLNSLNEPLVTMPIGYVTHGFN

Target LEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
2kqw.1.A LEEAARCMRSLKAPAVVSVSSPDAVTTYNGYLTSSSKTSEEHFVETVSLAGSYRDWSYSGQRTELGVEFLKRGDKIVYHT

Target -SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKT
2kqw.1.A LESPVEFHLDGEV-------------------------------------------------------------------

Target FYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQD
2kqw.1.A --------------------------------------------------------------------------------

Target AYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYE
2kqw.1.A --------------------------------------------------------------------------------

Target QFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSS
2kqw.1.A --------------------------------------------------------------------------------

Target EYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKF
2kqw.1.A --------------------------------------------------------------------------------

Target ADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTK
2kqw.1.A --------------------------------------------------------------------------------

Target PVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMA
2kqw.1.A --------------------------------------------------------------------------------

Target AYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLL
2kqw.1.A --------------------------------------------------------------------------------

Target QLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNL
2kqw.1.A --------------------------------------------------------------------------------

Target GMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRF
2kqw.1.A --------------------------------------------------------------------------------

Target FYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNR
2kqw.1.A --------------------------------------------------------------------------------

Target ATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVK
2kqw.1.A --------------------------------------------------------------------------------

Target NGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALV
2kqw.1.A --------------------------------------------------------------------------------

Target SDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKL
2kqw.1.A --------------------------------------------------------------------------------

Target SHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNN
2kqw.1.A --------------------------------------------------------------------------------

Target LPFKLTCATTRQVVNVVTTKIALKGG
2kqw.1.A --------------------------




Materials and Methods

Template Search

Template search with has been performed against the SWISS-MODEL template library (SMTL, last update: 2023-05-05, last included PDB release: 2023-04-28).

Model Building

Models are built based on the target-template alignment using ProMod3 (Studer et al.). Coordinates which are conserved between the target and the template are copied from the template to the model. Insertions and deletions are remodelled using a fragment library. Side chains are then rebuilt. Finally, the geometry of the resulting model is regularized by using a force field.

Model Quality Estimation

The global and per-residue model quality has been assessed using the QMEAN scoring function (Studer et al.).

Ligand Modelling

Ligands present in the template structure are transferred by homology to the model when the following criteria are met: (a) The ligands are annotated as biologically relevant in the template library, (b) the ligand is in contact with the model, (c) the ligand is not clashing with the protein, (d) the residues in contact with the ligand are conserved between the target and the template. If any of these four criteria is not satisfied, a certain ligand will not be included in the model. The model summary includes information on why and which ligand has not been included.

Oligomeric State Conservation

The quaternary structure annotation of the template is used to model the target sequence in its oligomeric form. The method (Bertoni et al.) is based on a supervised machine learning algorithm, Support Vector Machines (SVM), which combines interface conservation, structural clustering, and other template features to provide a quaternary structure quality estimate (QSQE). The QSQE score is a number between 0 and 1, reflecting the expected accuracy of the interchain contacts for a model built based a given alignment and template. Higher numbers indicate higher reliability. This complements the GMQE score which estimates the accuracy of the tertiary structure of the resulting model.

References

Table T1:

Primary amino acid sequence for which templates were searched and models were built.

APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLAS
HMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTP
VVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVV
GPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITES
KPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALR
KVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY
GARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSG
QSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTF
YVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYC
NKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKH
GTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQ
PYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLG
LKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYL
KSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDL
TAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRA
TRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSL
SHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEA
ELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDF
MSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGG

Table T2:

Template Seq Identity Oligo-state QSQE Found by Method Resolution Seq Similarity Coverage Description
6wuu.4.A 99.69 monomer - BLAST X-ray 2.79Å 0.62 0.16 Non-structural protein 3
6wuu.1.A 99.69 monomer - BLAST X-ray 2.79Å 0.62 0.16 Non-structural protein 3
6wuu.2.A 99.69 monomer - BLAST X-ray 2.79Å 0.62 0.16 Non-structural protein 3
7cmd.2.A 100.00 monomer - HHblits X-ray 2.59Å 0.63 0.16 Non-structural protein 3
6w9c.1.A 100.00 homo-trimer 0.26 HHblits X-ray 2.70Å 0.63 0.16 Non-structural protein 3
8eua.1.A 99.69 monomer - BLAST X-ray 3.10Å 0.62 0.16 Papain-like protease nsp3
7cmd.4.A 100.00 monomer - HHblits X-ray 2.59Å 0.63 0.16 Non-structural protein 3
7cmd.1.A 100.00 monomer - HHblits X-ray 2.59Å 0.63 0.16 Non-structural protein 3
7cmd.3.A 100.00 monomer - HHblits X-ray 2.59Å 0.63 0.16 Non-structural protein 3
5e6j.1.A 82.91 monomer - HHblits X-ray 2.85Å 0.57 0.16 Replicase polyprotein 1ab
7lfu.1.A 82.91 monomer - HHblits X-ray 2.29Å 0.57 0.16 papain-like protease
3e9s.1.A 82.86 monomer - HHblits X-ray 2.50Å 0.57 0.16 Non-structural protein 3
3e9s.1.A 82.86 monomer - BLAST X-ray 2.50Å 0.57 0.16 Non-structural protein 3
7lfv.2.A 82.91 monomer - HHblits X-ray 2.23Å 0.57 0.16 papain-like protease
5e6j.2.A 82.91 monomer - HHblits X-ray 2.85Å 0.57 0.16 Replicase polyprotein 1ab
7lfv.1.A 82.91 monomer - HHblits X-ray 2.23Å 0.57 0.16 papain-like protease
3mj5.1.A 82.86 monomer - HHblits X-ray 2.63Å 0.57 0.16 Replicase polyprotein 1a
8f2e.1.A 100.00 monomer - HHblits X-ray 2.43Å 0.61 0.15 Papain-like protease nsp3
4m0w.1.A 82.39 monomer - HHblits X-ray 1.40Å 0.56 0.16 Replicase polyprotein 1a
2w2g.1.A 75.00 homo-dimer 0.21 BLAST X-ray 2.22Å 0.53 0.14 NON-STRUCTURAL PROTEIN 3
2wct.1.A 75.00 homo-dimer 0.19 BLAST X-ray 2.79Å 0.53 0.14 NON-STRUCTURAL PROTEIN 3
2w2g.1.A 74.90 homo-dimer 0.21 HHblits X-ray 2.22Å 0.53 0.14 NON-STRUCTURAL PROTEIN 3
2wct.1.A 74.90 homo-dimer 0.19 HHblits X-ray 2.79Å 0.53 0.14 NON-STRUCTURAL PROTEIN 3
2w2g.1.B 75.00 homo-dimer 0.21 BLAST X-ray 2.22Å 0.53 0.14 NON-STRUCTURAL PROTEIN 3
2w2g.1.B 74.90 homo-dimer 0.20 HHblits X-ray 2.22Å 0.53 0.14 NON-STRUCTURAL PROTEIN 3
6ywk.4.A 100.00 monomer - BLAST X-ray 2.20Å 0.61 0.09 NSP3 macrodomain
6z5t.1.A 100.00 monomer - BLAST X-ray 1.57Å 0.61 0.09 Replicase polyprotein 1ab
6ywk.3.A 100.00 monomer - BLAST X-ray 2.20Å 0.61 0.09 NSP3 macrodomain
2acf.4.A 72.94 monomer - HHblits X-ray 1.40Å 0.52 0.09 Replicase polyprotein 1ab
2acf.4.A 73.37 monomer - BLAST X-ray 1.40Å 0.52 0.09 Replicase polyprotein 1ab
6ywk.1.A 100.00 monomer - BLAST X-ray 2.20Å 0.61 0.09 NSP3 macrodomain
7jme.1.A 100.00 monomer - BLAST X-ray 1.55Å 0.61 0.09 Non-structural protein 3
7c33.1.A 100.00 monomer - BLAST X-ray 3.83Å 0.61 0.09 Non-structural protein 3
2acf.2.A 72.94 monomer - HHblits X-ray 1.40Å 0.52 0.09 Replicase polyprotein 1ab
6wey.1.A 100.00 monomer - BLAST X-ray 0.95Å 0.61 0.09 Non-structural protein 3
2acf.2.A 73.37 monomer - BLAST X-ray 1.40Å 0.52 0.09 Replicase polyprotein 1ab
6woj.1.A 100.00 monomer - BLAST X-ray 2.20Å 0.61 0.09 Non-structural protein 3
2fav.2.A 73.81 monomer - BLAST X-ray 1.80Å 0.53 0.09 Replicase polyprotein 1ab (pp1ab) (ORF1AB)
2fav.1.A 73.81 monomer - BLAST X-ray 1.80Å 0.53 0.09 Replicase polyprotein 1ab (pp1ab) (ORF1AB)
2acf.1.A 73.37 monomer - BLAST X-ray 1.40Å 0.52 0.09 Replicase polyprotein 1ab
2acf.1.A 72.94 monomer - HHblits X-ray 1.40Å 0.52 0.09 Replicase polyprotein 1ab
7xc4.1.B 100.00 homo-dimer 0.24 HHblits X-ray 2.10Å 0.60 0.06 Papain-like protease nsp3
7xc3.1.B 100.00 homo-dimer 0.25 HHblits X-ray 1.70Å 0.61 0.06 Papain-like protease nsp3
7xc4.1.A 100.00 homo-dimer 0.25 BLAST X-ray 2.10Å 0.60 0.06 Papain-like protease nsp3
7xc4.1.A 100.00 homo-dimer 0.24 HHblits X-ray 2.10Å 0.60 0.06 Papain-like protease nsp3
7xc3.1.A 100.00 homo-dimer 0.25 HHblits X-ray 1.70Å 0.61 0.06 Papain-like protease nsp3
2kqv.1.A 78.13 monomer - HHblits NMR NA 0.55 0.10 Non-structural protein 3
7lgo.2.A 100.00 monomer - BLAST X-ray 2.45Å 0.64 0.06 Non-structural protein 3
7lgo.2.A 100.00 monomer - HHblits X-ray 2.45Å 0.64 0.06 Non-structural protein 3
7lgo.1.A 100.00 monomer - BLAST X-ray 2.45Å 0.64 0.06 Non-structural protein 3
7lgo.1.A 100.00 monomer - HHblits X-ray 2.45Å 0.64 0.06 Non-structural protein 3
2k87.1.A 81.74 monomer - BLAST NMR NA 0.58 0.06 Non-structural protein 3 of Replicase polyprotein 1a
2kqw.1.A 78.13 monomer - HHblits NMR NA 0.55 0.10 Non-structural protein 3
2kqw.1.A 80.22 monomer - BLAST NMR NA 0.55 0.09 Non-structural protein 3

The table above shows the top 54 filtered templates. A further 1,299 templates were found which were considered to be less suitable for modelling than the filtered list.
1hjz.2.A, 1njr.1.A, 1qmy.1.A, 1qol.3.A, 1qol.3.B, 1spv.1.A, 1txz.1.A, 1vhu.1.A, 1yd9.1.A, 1yd9.3.A, 1yd9.4.A, 1zr3.1.A, 1zr3.2.A, 1zr5.1.A, 2afc.1.A, 2dx6.1.A, 2eee.1.A, 2fav.1.A, 2fav.2.A, 2fav.3.A, 2fe8.1.A, 2fe8.2.A, 2fe8.3.A, 2fg1.1.A, 2fxk.2.A, 2gri.1.A, 2jqf.1.A, 2jqf.1.B, 2jqg.1.A, 2jzd.1.A, 2jzf.1.A, 2k87.1.A, 2kaf.1.A, 2kqv.1.A, 2l8r.1.A, 2lgr.1.A, 2m0a.1.A, 2vri.1.A, 2x47.1.A, 2xd7.1.A, 3ejf.1.A, 3ejg.1.A, 3eke.1.A, 3eti.1.A, 3ew5.1.A, 3ew5.2.A, 3ewo.1.A, 3ewo.1.B, 3ewr.1.A, 3gpo.1.A, 3gpq.4.A, 3gqe.1.A, 3gqe.2.A, 3gqo.3.A, 3gqo.4.A, 3iid.1.A, 3iif.1.A, 3iif.2.A, 3iif.3.A, 3j8h.1.A, 3jzt.1.A, 3mp2.1.A, 3q6z.1.A, 3q71.1.A, 3sih.1.A, 3sij.1.A, 3v2b.1.A, 3v45.1.A, 3vfq.1.A, 4abk.1.A, 4ess.1.A, 4etj.1.A, 4etk.1.A, 4etk.2.A, 4gua.1.A, 4gvv.1.A, 4gvv.2.A, 4gvv.3.A, 4gvw.1.A, 4iqy.1.A, 4j4z.1.A, 4j5q.1.A, 4j5r.1.A, 4j5s.1.A, 4jca.2.A, 4jgk.1.A, 4jgk.3.A, 4jll.1.A, 4jvv.1.A, 4k0c.1.A, 4k0c.2.A, 4kyb.1.A, 4kyb.2.A, 4mm3.1.B, 4ovz.1.A, 4ovz.2.A, 4ow0.1.A, 4p16.1.A, 4pt5.1.A, 4r3d.1.A, 4rez.1.A, 4rf0.1.A, 4rna.1.A, 4tu0.3.A, 4uml.1.A, 4wur.1.A, 4x2z.1.A, 4ypt.1.A, 5ail.1.A, 5bz0.1.A, 5cb3.1.A, 5cb5.1.A, 5cms.1.A, 5dus.1.A, 5e3b.1.A, 5fsu.1.A, 5fsu.2.A, 5fsz.1.A, 5fud.1.A, 5gky.1.E, 5gkz.1.G, 5gl0.1.A, 5gl1.1.A, 5hih.1.A, 5iit.1.A, 5iq5.1.A, 5isn.1.A, 5j8v.1.D, 5kiv.1.A, 5ko3.1.A, 5l9k.1.A, 5lau.1.A, 5lbp.1.A, 5lcc.1.A, 5lcc.2.A, 5lnc.1.A, 5lnc.2.A, 5lw0.1.A, 5lw6.1.A, 5m31.1.A, 5m3e.1.A, 5m3i.1.A, 5mqx.1.A, 5o2d.1.A, 5rs7.1.A, 5rs7.2.A, 5rs8.1.A, 5rs8.2.A, 5rs9.1.A, 5rs9.2.A, 5rsb.1.A, 5rsb.2.A, 5rsc.1.A, 5rsc.2.A, 5rsd.1.A, 5rsd.2.A, 5rse.1.A, 5rse.2.A, 5rsf.1.A, 5rsf.2.A, 5rsg.1.A, 5rsg.2.A, 5rsh.1.A, 5rsh.2.A, 5rsi.1.A, 5rsi.2.A, 5rsj.1.A, 5rsj.2.A, 5rsk.1.A, 5rsk.2.A, 5rsl.1.A, 5rsl.2.A, 5rsm.1.A, 5rsm.2.A, 5rsn.1.A, 5rsn.2.A, 5rso.1.A, 5rso.2.A, 5rsp.1.A, 5rsp.2.A, 5rsq.1.A, 5rsq.2.A, 5rsr.1.A, 5rsr.2.A, 5rss.1.A, 5rss.2.A, 5rst.1.A, 5rst.2.A, 5rsu.1.A, 5rsu.2.A, 5rsv.1.A, 5rsv.2.A, 5rsw.1.A, 5rsw.2.A, 5rsx.1.A, 5rsx.2.A, 5rsy.1.A, 5rsy.2.A, 5rsz.1.A, 5rsz.2.A, 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