3C-like proteinase nsp5 (3CL-PRO) | P0DTD1 PRO_0000449623

Homology Modelling Report

Model Building Report

This document lists the results for the homology modelling project "3C-like proteinase nsp5 (3CL-PRO) | P0DTD1 PRO_0000449623" submitted to SWISS-MODEL workspace on May 5, 2023, 9:34 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:

Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T
SWISS-MODEL: homology modelling of protein structures and complexes.
Nucleic Acids Res 46, W296-W303. (2018) 29788355 10.1093/nar/gky427
Bienert S, Waterhouse A, de Beer TAP, Tauriello G, Studer G, Bordoli L, Schwede T
The SWISS-MODEL Repository - new features and functionality.
Nucleic Acids Res 45, D313-D319. (2017) 27899672 10.1093/nar/gkw1132
Studer G, Tauriello G, Bienert S, Biasini M, Johner N, Schwede T
ProMod3 - A versatile homology modelling toolbox.
PLOS Comp Biol 17(1), e1008667. (2021) 33507980 10.1371/journal.pcbi.1008667
Studer G, Rempfer C, Waterhouse AM, Gumienny R, Haas J, Schwede T
QMEANDisCo - distance constraints applied on model quality estimation.
Bioinformatics 36, 1765-1771. (2020) 31697312 10.1093/bioinformatics/btz828
Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology.
Scientific Reports 7. (2017) 28874689 10.1038/s41598-017-09654-8

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 2024 templates were found (Table T2).

Models

The following model was built (see Materials and Methods "Model Building"):

Model #02	File	Built with	Oligo-State	Ligands	GMQE	QMEANDisCo Global
	PDB	ProMod3 3.3.0	homo-dimer (matching prediction)	2 x T8J: 1-[4-(thiophene-2-carbonyl)piperazin-1-yl]ethan-1-one;	0.97	0.91 ± 0.05

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Range	Coverage	Description
5rfv.1.B	100.00	homo-dimer	0.95	HHblits	X-ray	1.48Å	0.63	1 - 304	1.00	3C-like proteinase

Included Ligands

Ligand	Description
2 x T8J	1-[4-(thiophene-2-carbonyl)piperazin-1-yl]ethan-1-one

Excluded ligands

Ligand Name.Number	Reason for Exclusion	Description
DMS.1	Not biologically relevant.	DIMETHYL SULFOXIDE
DMS.2	Not biologically relevant.	DIMETHYL SULFOXIDE
DMS.3	Not biologically relevant.	DIMETHYL SULFOXIDE
DMS.5	Not biologically relevant.	DIMETHYL SULFOXIDE
DMS.6	Not biologically relevant.	DIMETHYL SULFOXIDE
DMS.7	Not biologically relevant.	DIMETHYL SULFOXIDE

Target    SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGH
5rfv.1.B  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGH

Target    SMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFC
5rfv.1.B  SMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFC

Target    YMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
5rfv.1.B  YMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE

Target    PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ
5rfv.1.B  PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ


Target    SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGH
5rfv.1.B  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGH

Target    SMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFC
5rfv.1.B  SMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFC

Target    YMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
5rfv.1.B  YMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE

Target    PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ
5rfv.1.B  PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

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

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL
BLAST+: architecture and applications.
BMC Bioinformatics, 10, 421-430. (2009) 20003500 10.1186/1471-2105-10-421
Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J
HH-suite3 for fast remote homology detection and deep protein annotation.
BMC Bioinformatics 20, 473. (2019) 31521110 10.1186/s12859-019-3019-7

Table T1:

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Table T2:

Template	Seq Identity	Oligo-state	QSQE	Found by	Method	Resolution	Seq Similarity	Coverage	Description
6lu7.1.B	100.00	homo-dimer	0.99	HHblits	X-ray	2.16Å	0.63	1.00	3C-like proteinase
6y2g.1.B	100.00	homo-dimer	1.00	HHblits	X-ray	2.20Å	0.63	1.00	3C-like proteinase
5ree.1.A	100.00	homo-dimer	0.98	HHblits	X-ray	1.77Å	0.63	1.00	3C-like proteinase
5rea.1.A	100.00	homo-dimer	0.98	HHblits	X-ray	1.63Å	0.63	1.00	3C-like proteinase
5r7z.1.B	100.00	homo-dimer	0.97	HHblits	X-ray	1.59Å	0.63	1.00	3C-like proteinase
5rfe.1.B	100.00	homo-dimer	0.96	HHblits	X-ray	1.46Å	0.63	1.00	3C-like proteinase
5rgk.1.A	100.00	homo-dimer	0.96	HHblits	X-ray	1.43Å	0.63	1.00	3C-like proteinase
5r8t.1.A	100.00	homo-dimer	0.96	HHblits	X-ray	1.27Å	0.63	1.00	3C-like proteinase
5r8t.1.B	100.00	homo-dimer	0.96	HHblits	X-ray	1.27Å	0.63	1.00	3C-like proteinase
5rgo.1.B	100.00	homo-dimer	0.96	HHblits	X-ray	1.74Å	0.63	1.00	3C-like proteinase
5rfv.1.B	100.00	homo-dimer	0.95	HHblits	X-ray	1.48Å	0.63	1.00	3C-like proteinase
5rfl.1.B	100.00	homo-dimer	0.95	HHblits	X-ray	1.64Å	0.63	1.00	3C-like proteinase
2z9j.1.A	96.08	homo-dimer	0.95	HHblits	X-ray	1.95Å	0.62	1.00	3C-like proteinase
2a5i.1.A	96.08	homo-dimer	0.92	HHblits	X-ray	1.88Å	0.62	1.00	3C-like peptidase

The table above shows the top 14 filtered templates. A further 1,938 templates were found which were considered to be less suitable for modelling than the filtered list.
1f5t.1.C, 1f5t.1.D, 1i1g.1.A, 1i1g.1.B, 1j75.1.A, 1ku9.1.A, 1lnw.1.A, 1lnw.1.B, 1lnw.2.A, 1lnw.2.B, 1lnw.3.A, 1lnw.3.B, 1lnw.4.A, 1lnw.4.B, 1lq1.1.C, 1lq1.1.D, 1lq1.2.D, 1lvb.1.A, 1lvo.1.A, 1lvo.1.B, 1lvo.2.A, 1lvo.2.B, 1lvo.3.B, 1mj9.1.A, 1mja.1.A, 1mjb.1.A, 1mkm.1.A, 1mkm.1.B, 1nd9.1.A, 1nex.2.A, 1oyi.1.A, 1p4x.1.A, 1p9s.1.A, 1q2w.1.A, 1q2w.1.B, 1q31.1.A, 1q31.2.A, 1r1t.1.A, 1r1t.1.B, 1ri7.1.A, 1s3j.1.A, 1s3j.1.B, 1sfu.1.A, 1sfu.1.B, 1sfx.1.A, 1sfx.1.B, 1smt.1.A, 1ub9.1.A, 1uj1.1.B, 1uk3.1.A, 1uk3.1.B, 1wi9.1.A, 1xd7.1.A, 1xn7.1.A, 1ylf.1.A, 1ylf.1.B, 1ylf.1.C, 1z1i.1.A, 1z1j.1.A, 1z1j.1.B, 1z67.1.A, 2a5k.1.A, 2alv.1.A, 2amd.1.A, 2amd.1.B, 2amp.1.A, 2bx3.1.B, 2bx4.1.B, 2c3s.1.A, 2cfx.1.A, 2cg4.1.A, 2cyy.1.A, 2d1h.1.A, 2d1h.1.B, 2dbb.1.A, 2dbb.1.B, 2du9.1.A, 2duc.1.A, 2e1c.1.D, 2e7w.1.A, 2e7x.1.A, 2efn.1.A, 2efo.1.A, 2efp.1.A, 2efq.1.A, 2ek5.1.B, 2ek5.3.A, 2ek5.4.A, 2ek5.4.B, 2eth.1.A, 2eth.1.B, 2fbi.1.A, 2gt8.1.A, 2gtb.1.A, 2heo.1.A, 2heo.1.B, 2htj.1.A, 2ia0.1.A, 2ia0.1.B, 2ivm.1.A, 2ivm.1.B, 2jt1.1.A, 2k02.1.A, 2k53.1.A, 2k7x.1.A, 2l02.1.A, 2l02.1.B, 2l4a.1.A, 2l54.1.A, 2lfc.1.A, 2liz.1.A, 2lnb.1.A, 2mlg.1.A, 2obp.1.A, 2op9.1.A, 2op9.1.B, 2p5v.1.A, 2p5v.1.C, 2p5v.1.D, 2p6s.1.B, 2p6s.1.D, 2p6s.1.F, 2p6t.1.E, 2p6t.1.G, 2p6t.1.H, 2pmh.1.A, 2pn6.1.A, 2pwx.1.A, 2q6d.1.A, 2q6d.1.B, 2q6d.2.A, 2q6f.1.B, 2q6g.1.A, 2q6g.1.B, 2qc2.1.A, 2qc2.1.B, 2qcy.1.A, 2qiq.1.A, 2qz8.1.A, 2rvc.1.A, 2v79.1.A, 2v79.1.B, 2vj1.1.A, 2vj1.1.B, 2w24.1.A, 2w24.1.B, 2w25.1.A, 2w25.1.B, 2w29.1.A, 2w29.1.B, 2wkj.1.A, 2xvc.1.A, 2y75.1.A, 2y75.1.B, 2yna.1.A, 2z9j.1.B, 2zny.1.A, 2zny.1.B, 2zny.2.A, 2zny.2.B, 2zny.3.A, 2zny.4.A, 2zny.4.B, 2znz.1.A, 2znz.1.B, 2znz.1.D, 2zu2.1.A, 3aw1.1.A, 3aw1.1.B, 3bj6.1.A, 3d23.1.A, 3d23.1.C, 3d62.1.A, 3dpl.1.A, 3dqv.1.B, 3dqv.3.B, 3e91.1.A, 3ea7.1.B, 3ea8.1.A, 3ea9.1.A, 3ebn.1.A, 3ebn.2.A, 3ech.1.A, 3ech.1.B, 3eco.1.A, 3eco.1.B, 3f9e.1.A, 3f9f.1.A, 3f9g.1.A, 3f9g.1.B, 3f9h.1.B, 3fzd.1.A, 3gfl.1.A, 3i4p.1.A, 3i71.1.A, 3i71.1.B, 3iwm.1.E, 3iwm.1.F, 3iwm.1.G, 3iwm.1.H, 3k69.1.A, 3ke2.1.A, 3ke2.2.A, 3lwf.1.A, 3m3s.1.A, 3m3t.1.A, 3m3v.1.A, 3m3v.1.B, 3mex.1.A, 3mex.1.B, 3mks.2.A, 3mks.3.A, 3mmg.1.A, 3mmg.2.A, 3o3k.1.A, 3q5f.1.A, 3qph.1.A, 3qpt.1.A, 3s2w.1.A, 3s2w.1.B, 3s2w.2.A, 3s2w.2.B, 3s2w.3.A, 3s2w.3.B, 3s2w.4.A, 3s2w.4.B, 3sna.1.A, 3t8r.1.A, 3tlo.1.A, 3tlo.1.B, 3to6.1.A, 3to9.1.A, 3v7d.1.A, 3v7d.2.A, 3vb2.1.A, 3vb2.1.B, 3vb3.1.A, 3vod.1.A, 3vod.1.B, 4awx.1.B, 4ch7.1.A, 4czd.1.A, 4czd.1.B, 4czd.2.A, 4czd.2.B, 4egy.1.A, 4egz.1.A, 4egz.1.B, 4f49.1.A, 4fht.1.A, 4fht.1.B, 4g9y.1.A, 4ggg.1.A, 4ggg.2.A, 4ham.1.A, 4hi3.1.A, 4hi3.1.B, 4hob.1.A, 4hob.1.B, 4hob.2.A, 4jba.1.A, 4kmf.1.A, 4lb5.1.A, 4lb6.1.A, 4mds.1.A, 4pcq.1.A, 4pcq.1.B, 4pcq.2.A, 4pcq.2.B, 4pql.1.A, 4pql.1.B, 4pt7.1.A, 4rs8.1.A, 4rs8.1.B, 4rsp.2.A, 4tww.1.B, 4u0y.1.A, 4u0y.1.B, 4u0y.1.D, 4wmd.1.A, 4wmd.1.B, 4wme.1.A, 4wmf.2.C, 4xfq.1.A, 4xfq.1.B, 4ylu.1.A, 4ylu.1.B, 4yo9.1.B, 4yog.1.B, 4yoi.1.A, 4zro.1.A, 4zro.1.B, 4zro.1.C, 4zro.1.D, 4zuh.1.A, 4zuh.1.B, 4zzl.1.A, 4zzl.1.B, 5b6o.1.A, 5b6o.1.B, 5bpd.1.A, 5bpd.1.C, 5bqt.1.A, 5bqt.1.B, 5bqt.1.C, 5bqt.1.D, 5c0t.1.A, 5c0t.2.A, 5c17.1.A, 5c3n.1.A, 5c3n.1.B, 5d4r.2.A, 5d4s.2.B, 5eu8.1.A, 5gwy.1.A, 5gwy.1.B, 5gwz.1.A, 5hsm.1.A, 5hso.1.A, 5hyo.1.A, 5hyo.1.B, 5j6x.1.A, 5k1y.1.A, 5k1y.1.B, 5k1y.1.C, 5k1y.1.D, 5k1y.1.G, 5k1y.1.H, 5k5q.1.A, 5k5q.1.B, 5k5q.1.C, 5k5q.1.D, 5k5q.1.G, 5k5q.1.H, 5kbj.1.A, 5kbj.1.B, 5kbj.1.C, 5kbj.1.D, 5kbj.2.A, 5kbj.2.B, 5kbj.2.C, 5kbj.2.D, 5kk1.1.A, 5kvr.1.A, 5n07.1.A, 5nh0.1.A, 5r7y.1.A, 5r7y.1.B, 5r7z.1.A, 5r80.1.A, 5r80.1.B, 5r81.1.A, 5r81.1.B, 5r82.1.A, 5r82.1.B, 5r83.1.A, 5r83.1.B, 5r84.1.A, 5r84.1.B, 5re4.1.A, 5re4.1.B, 5re5.1.A, 5re5.1.B, 5re6.1.A, 5re6.1.B, 5re7.1.A, 5re7.1.B, 5re8.1.A, 5re8.1.B, 5re9.1.A, 5re9.1.B, 5rea.1.B, 5reb.1.A, 5reb.1.B, 5rec.1.A, 5rec.1.B, 5red.1.A, 5red.1.B, 5ree.1.B, 5ref.1.A, 5ref.1.B, 5reg.1.A, 5reg.1.B, 5reh.1.A, 5reh.1.B, 5rei.1.A, 5rei.1.B, 5rej.1.A, 5rej.1.B, 5rek.1.A, 5rek.1.B, 5rel.1.A, 5rel.1.B, 5rem.1.A, 5rem.1.B, 5ren.1.A, 5ren.1.B, 5reo.1.A, 5reo.1.B, 5rep.1.A, 5rep.1.B, 5rer.1.A, 5rer.1.B, 5res.1.A, 5res.1.B, 5ret.1.A, 5ret.1.B, 5reu.1.A, 5reu.1.B, 5rev.1.A, 5rev.1.B, 5rew.1.A, 5rew.1.B, 5rex.1.A, 5rex.1.B, 5rey.1.A, 5rey.1.B, 5rez.1.A, 5rez.1.B, 5rf0.1.A, 5rf0.1.B, 5rf1.1.A, 5rf1.1.B, 5rf2.1.A, 5rf2.1.B, 5rf3.1.A, 5rf3.1.B, 5rf4.1.A, 5rf4.1.B, 5rf5.1.A, 5rf5.1.B, 5rf6.1.A, 5rf6.1.B, 5rf7.1.A, 5rf7.1.B, 5rf8.1.A, 5rf8.1.B, 5rf9.1.A, 5rf9.1.B, 5rfa.1.A, 5rfa.1.B, 5rfb.1.A, 5rfb.1.B, 5rfc.1.A, 5rfc.1.B, 5rfd.1.A, 5rfd.1.B, 5rfe.1.A, 5rff.1.A, 5rff.1.B, 5rfg.1.A, 5rfg.1.B, 5rfh.1.A, 5rfh.1.B, 5rfi.1.A, 5rfi.1.B, 5rfj.1.A, 5rfj.1.B, 5rfk.1.A, 5rfk.1.B, 5rfl.1.A, 5rfm.1.A, 5rfm.1.B, 5rfn.1.A, 5rfn.1.B, 5rfo.1.A, 5rfo.1.B, 5rfp.1.A, 5rfp.1.B, 5rfq.1.A, 5rfq.1.B, 5rfr.1.A, 5rfr.1.B, 5rfs.1.A, 5rfs.1.B, 5rft.1.A, 5rft.1.B, 5rfu.1.A, 5rfu.1.B, 5rfv.1.A, 5rfw.1.A, 5rfw.1.B, 5rfx.1.A, 5rfx.1.B, 5rfy.1.A, 5rfy.1.B, 5rfz.1.A, 5rfz.1.B, 5rg0.1.A, 5rg0.1.B, 5rg1.1.A, 5rg1.1.B, 5rg2.1.A, 5rg2.1.B, 5rg3.1.A, 5rg3.1.B, 5rgg.1.A, 5rgg.1.B, 5rgh.1.A, 5rgh.1.B, 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