SWISS-MODEL Repository 
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SWISS-MODEL Repository - Model Details
Model Overview
Sequence
Domain
Model 3D Structure
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Template Links:
[ RCSB ]
[ PDBe ]
[ SCOP ]
[ CATH ]
display model: in [ AstexViewer ] download model: as [ pdb ] - as [ Deepview project ] 
This model has not been updated since 2013-01-30. In the meantime, new template
structures may have become available which would allow building a more reliable model.
Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now?
[ Submit ]
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Alignment
TARGET 1 RD KILKWNGWGY SDSQFAINKD GHVTFTGDKY EISGKVMPHF
4bby_1#1 81 giipkk--rq elmkwngwgy ndskfflnkk gqleltgkry plsgvalptf
TARGET sss ss s sssss sssss sss
4bby_1#1 sss ss s sssss sssss hh
TARGET 43 RPWFENYLGI DLGFVSPAQK LSDVIIDAP- -VENEDIIEF LQENKISFSN
4bby_1#1 129 kdwiqntfgi nl-------- --dhktdtpp sivnedflhe lkktnisysq
TARGET sssss hhhhh sss
4bby_1#1 hhhhhhh hhhhhh hhh sss
TARGET 91 EARIRLMRGH GHTVHDMINL REGKIPRLPD IVVWPKSEHE IVKIIEGAMS
4bby_1#1 178 eaddrvfrah ghclheifll regmferipd ivlwptchdd vvkivnlack
TARGET hhhhh hhhhhhh h ssss hhh hhhhhhhhhh
4bby_1#1 hhhhhhh hhhhhhh h ssss hhh hhhhhhhhhh
TARGET 141 HNCAIIPIGG GTSVTNALDT PETEKRAVIS MDMALLDKIL WIDRENLTCR
4bby_1#1 228 ynlciipigg gtsvsyglmc padetrtiis ldtsqmnril wvdennltah
TARGET sssss ssss sss sssss sss ssss
4bby_1#1 h sssss ssss sss sssss sss ssss
TARGET 191 AQAGIVGQSL ERQLNKKGFT CGHEPDSIEF STLGGWVSTR ASGMKKNKYG
4bby_1#1 278 veagitgqel erqlkesgyc tghepdslef stvggwistr asgmkkniyg
TARGET ssss hhhh hhhhhhhsss hhhhhh hhh
4bby_1#1 ssss hhhh hhhhhhhsss hhhhhh hhh
TARGET 241 NIEDLVVHLN FVCPKGIIQK QCQVPRMSSG PDIHQIILGS EGTLGVVSEV
4bby_1#1 328 niedlvvhmk vvtprgviek scqgprmstg pdihhfimgs egtlgvitea
TARGET hhhssssss sss sss hhhh sssss
4bby_1#1 hhhssssss sss sss hhhh sssss
TARGET 291 TIKIFPIPEV KRFGSFVFPN FESGVNFFRE VAIQRCQPAS LRLMDNDQFV
4bby_1#1 378 tikirptpey qkygsvafpn feqgvaclre iakqrcapas irlmdnqqfq
TARGET sssssss s ssssssss hhhhhhhhhh hhhh s ssssshhhhh
4bby_1#1 sssssss s ssssssss hhhhhhhhhh hhhh s ssssshhhhh
TARGET 341 MGQALKVASD SWWADLKSSV SKMYITSWKG FKVDEICAAT CVYEGNREEV
4bby_1#1 428 fgha------ -----lkpqv ssifts---g fdpnqlsvat llfegdrekv
TARGET hhhh sss sss ssss sssss hhhh
4bby_1#1 hhhh ssss sssss hhhh
TARGET 391 DQHEERLNKL AEQFHGVVGG AENGQYGYRL TFAIAYLRDL GMNHGVLGES
4bby_1#1 478 lqhekqvydi aakfgglaag edngqrgyll tyviaymrdl gleyyiiges
TARGET hhhhhhhhhh hh sss hhhhhhh hhhhhhhhhh hh ssssss
4bby_1#1 hhhhhhhhhh hh sss hhhhhhhhhh hhhhhhhhhh hh ssssss
TARGET 441 FETSVPWDKV LSLCRNVKEL MKREAKAQGV THPVLANCRV TQVYDAGACV
4bby_1#1 528 fetsapwdrv vdlcrnvker irreckekgv qfpplstcrv tqtydagaci
TARGET sssss hhh hhhhhhhhhh hhhhhhhh ssssss ssss ssss
4bby_1#1 sssss hhh hhhhhhhhhh hhhhhhhh ssssss ssss ssss
TARGET 491 YFYFGFNARG LKNGLEVYDR IETAARDEII ACGGSISHHH GVGKIRKQWM
4bby_1#1 578 yfyfafnyrg isdplavfeq teaaareeil anggslshhh gvgklrkqwl
TARGET ssssssss hhhhhhh hhhhhhhhhh h
4bby_1#1 ssssssss hhhhhhh hhhhhhhhhh h
TARGET 541 LTTNGAVGIA LLKAIKSELD PANIFASANL I ------- RDKILKWNGW
4bby_1#1 628 kesisdvgfg mlksvkdyvd ptnifgnrnl l-giipkk-- rqelmkwngw
*
TARGET hh hhhhh hhhhhhhhh sss
4bby_1#1 hh hhhhh hhhhhhhhh sss
TARGET 582 GYSDSQFAIN KDGHVTFTGD KYEISGKVMP HFRPWFENYL GIDLGFVSPA
4bby_1#1 97 gyndskffln kkgqleltgk ryplsgvalp tfkdwiqntf ginl---tpp
TARGET sss sssss sssss ssss sss ssssssss hhhh
4bby_1#1 sss sssss sssss hhhhhhhhh
TARGET 632 QKLSDVIIDA PVENEDIIEF LQENKISFSN EARIRLMRGH GHTVHDMINL
4bby_1#1 158 s--------- -ivnedflhe lkktnisysq eaddrvfrah ghclheifll
TARGET hhhhhhhhhh hhhh sss hhhhh hhhhhhh
4bby_1#1 hhhhhh hhh sss hhhhh hhhhhhh
TARGET 682 REGKIPRLPD IVVWPKSEHE IVKIIEGAMS HNCAIIPIGG GTSVTNALDT
4bby_1#1 198 regmferipd ivlwptchdd vvkivnlack ynlciipigg gtsvsyglmc
TARGET h ssss hhh hhhhhhhhhh sssss
4bby_1#1 hh ssss hhh hhhhhhhhhh h sssss
TARGET 732 PETEKRAVIS MDMALLDKIL WIDRENLTCR AQAGIVGQSL ERQLNKKGFT
4bby_1#1 248 padetrtiis ldtsqmnril wvdennltah veagitgqel erqlkesgyc
TARGET ssss sss sssss sss ssss ssss hhhh hhhhhhhsss
4bby_1#1 ssss sss sssss sss ssss ssss hhhh hhhhhh sss
TARGET 782 CGHEPDSIEF STLGGWVSTR ASGMKKNKYG NIEDLVVHLN FVCPKGIIQK
4bby_1#1 298 tghepdslef stvggwistr asgmkkniyg niedlvvhmk vvtprgviek
TARGET hhhhhh hhh hhhssssss sss sss
4bby_1#1 hhhhhh hhh hhhssssss sss sss
TARGET 832 QCQVPRMSSG PDIHQIILGS EGTLGVVSEV TIKIFPIPEV KRFGSFVFPN
4bby_1#1 348 scqgprmstg pdihhfimgs egtlgvitea tikirptpey qkygsvafpn
TARGET hhhh sssss sssssss s ssssssss
4bby_1#1 hhhh sssss sssssss s ssssssss
TARGET 882 FESGVNFFRE VAIQRCQPAS LRLMDNDQFV MGQALKVASD SWWADLKSSV
4bby_1#1 398 feqgvaclre iakqrcapas irlmdnqqfq fghalkp--- ----------
TARGET hhhhhhhhhh hhhh s ssssshhhhh hhh
4bby_1#1 hhhhhhhhh hhhh s ssssshhhhh hhhh
TARGET 932 SKMYITSWKG FKVDEICAAT CVYEGNREEV DQHEERLNKL AEQFHGVVGG
4bby_1#1 435 --------qg fdpnqlsvat llfegdrekv lqhekqvydi aakfgglaag
TARGET hhhhhhhhh ssss sssss hhhh hhhhhhhhhh hh sss
4bby_1#1 ssss sssss hhhh hhhhhhhhhh hh sss
TARGET 982 AENGQYGYRL TFAIAYLRDL GMNHGVLGES FETSVPWDKV LSLCRNVKEL
4bby_1#1 498 edngqrgyll tyviaymrdl gleyyiiges fetsapwdrv vdlcrnvker
TARGET hhhhhhhhhh hhhhhh hh ssssss sssss h hhhhhhhhhh
4bby_1#1 hhhhhh h hhhhhhh hh ssssss sssss hhhhhhhhhh
TARGET 1032 MKREAKAQGV THPVLANCRV TQVYDAGACV YFYFGFNARG LKNGLEVYDR
4bby_1#1 548 irreckekgv qfpplstcrv tqtydagaci yfyfafnyrg isdplavfeq
TARGET hhhhhhhh ssssss ssss ssss ssssssss hhhhhhh
4bby_1#1 hhhhhhhh ssssss ssss ssss ssssssss hhhhhhh
TARGET 1082 IETAARDEII ACGGSISHHH GVGKIRKQWM LTTNGAVGIA LLKAIKSELD
4bby_1#1 598 teaaareeil anggslshhh gvgklrkqwl kesisdvgfg mlksvkdyvd
TARGET hhhhhhhhhh h hh hhhhh hhhhhhhhh
4bby_1#1 hhhhhhhhhh h hh hhhhh hhhhhhhhh
TARGET 1132 PANIFASANL I
4bby_1#1 648 ptnifgnrnl l-
TARGET
4bby_1#1
Template's ligands section
Ligands in the template:FAD : 2,SO4 : 3.
Ligands in the template that will be assessed: FAD1, FAD231.
Model's ligands section
FAD1
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand z.FAD1 will not be included in the model.
FAD1: conservation:False, RMSD:False, included: False
FAD231
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand z.FAD231 will not be included in the model.
FAD231: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
4bby is annotated as DIMER
The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry
The following biological unit was used to build the template structure: 4bby.pdb1.gz
Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template can be assumed to be similar (=DIMER)
The corresponding reliability score is 0.882 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 4bbyB
Model was succesfully built as DIMER.
Template Selection
- Start SMR-Pipeline for:49b7e19a671817a73c2882852b441d6e on BC2-cluster at Wed Feb 20 20:24:23
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- No template with D found
- No template with C found
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:1): model based on new templates
- Send 1 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *****************************************************************************
- building model based on 4bbyA (17-587) was successful
- Repository Pipeline parameter
Cut-off parameters to model the target based on a BLAST target-template alignment
Evalue : 0.0001
Minimum Template size (aa) for ranking : 25
Minimum Sequence identity : 60
Cut-off parameters to model the target based on a HHSearch target-template alignment
Evalue : 0.0001
Probability : 50
MAC : 0.3
Parameters for model selection
Minimal number of uncovered target
residues after BLAST to run HHSEARCH : 50
Minimal number of uncovered target
residues to model an additional template : 25
- Finish SMR-Pipeline for:49b7e19a671817a73c2882852b441d6e on BC2-cluster at Wed Feb 20 20:40:27
2013
Template Search
| Template Description |
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4bc9: MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: WILD- TYPE, ADDUCT WITH CYANOETHYL Solved by: X-RAY, Resolution: 2.41A, Identified by HHSEARCH |
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4bby: MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: WILD-TY Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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4bca: MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: TYR578PHE MUTANT Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH |
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4bc7: MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: ARG419HIS MUTANT Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH |
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Downloads
Reference
If you are using models from the SWISS-MODEL Repository, please cite the following articles:
- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.
- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.