SWISS-MODEL Repository
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
| UniProt | O55125 |
Database: TrEMBL (Unreviewed)  |
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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 YELRTYKLKP GTMIEWGNNW -ARAIKYRQE N-QEAVGGFF
1vqs_1#1 65531 hhhhhhxf-- yeirtyrlkn gaipaylkvv edegieiqks hlgelvgyff
TARGET sssssssss hhhhhhh hhhhh sssssss
1vqs_1#1 s sssssssss hhhhhhhh h hhhhhh hh sssssss
TARGET 39 SQIGELYVVH HLWAYKDLQS REETRNAAWR KRGWDENVYY TVPLVRHMES
1vqs_1#1 43 seigpineiv hiwafssldd raerrarlxa dprwlsflpk irdlievaen
TARGET ss sssssss ssss hhh hhhhhhhhh hhhhhhh sssssss
1vqs_1#1 ss sssssss sssss hhh hhhhhhhh hhhhhhhh sssssss
TARGET 89 RIMIPLKISP L -------- --- YELRTY KLKPGTMIEW GNNW-ARAIK
1vqs_1#1 93 kixkparfsp l-xihhhhhh xf--yeirty rlkngaipay lkvvedegie
*
TARGET ssssss ssssss sss hhhh hh
1vqs_1#1 ssssss s ssssss sss hhhh hhhhh hh
TARGET 125 YRQEN-QEAV GGFFSQIGEL YVVHHLWAYK DLQSREETRN AAWRKRGWDE
1vqs_1#1 29 iqkshlgelv gyffseigpi neivhiwafs slddraerra rlxadprwls
TARGET sss ssssss sss ssssssss hhhhhhhhh hhh hhhh
1vqs_1#1 hhhhhh sss ssssss sss sssssssss hhhhhhhhh hhh hhhh
TARGET 174 NVYYTVPLVR HMESRIMIPL KISPL ---- ------ YEL RTYKLKPGTM
1vqs_1#1 79 flpkirdlie vaenkixkpa rfspl-xhhh hhhxf--yei rtyrlkngai
*
TARGET hhh sss ssssssssss sss ssssss h
1vqs_1#1 hhh sss ssssssssss s sss ssssss h
TARGET 212 IEWGNNW-AR AIKYRQEN-Q EAVGGFFSQI GELYVVHHLW AYKDLQSREE
1vqs_1#1 16 paylkvvede gieiqkshlg elvgyffsei gpineivhiw afsslddrae
TARGET hhhhhh hhhhh sssssssss ssssssssss s hhhhhh
1vqs_1#1 hhhhhhhh hhhhhhhh sssssssss ssssssssss ss hhhhhh
TARGET 260 TRNAAWRKRG WDENVYYTVP LVRHMESRIM IPLKISPL - ----------
1vqs_1#1 66 rrarlxadpr wlsflpkird lievaenkix kparfspl-x ihhhhhhxf-
*
TARGET hhhhhh h hhhhhh ssssssssss sss
1vqs_1#1 hhhhh hh hhhhhh ssssssssss sss s
TARGET 298 YELRTYKLK PGTMIEWGNN W-ARAIKYRQ EN-QEAVGGF FSQIGELYVV
1vqs_1#1 3 -yeirtyrlk ngaipaylkv vedegieiqk shlgelvgyf fseigpinei
TARGET sssssssss hhhhhh ssssss sss ssssss
1vqs_1#1 sssssssss hhhhhhh hh hhhhh hhh ssssss sss ssssss
TARGET 345 HHLWAYKDLQ SREETRNAAW RKRGWDENVY YTVPLVRHME SRIMIPLKIS
1vqs_1#1 52 vhiwafssld draerrarlx adprwlsflp kirdlievae nkixkparfs
TARGET sssss hh hhhhhhhhhh hhhhhhh ssssss sssssss
1vqs_1#1 ssssss hh hhhhhhhhhh hhhhhhh ssssss sssssss
TARGET 395 PL ------- --- YELRTY KLKPGTMIEW GNNW-ARAIK YRQEN-QEAV
1vqs_1#1 102 pl-xhhhhhh xf--yeirty rlkngaipay lkvvedegie iqkshlgelv
*
TARGET ssssss sss hhhh hhh hh hhh sss
1vqs_1#1 s ssssss sss hhhh hhhhh hh hhhhhh sss
TARGET 431 GGFFSQIGEL YVVHHLWAYK DLQSREETRN AAWRKRGWDE NVYYTVPLVR
1vqs_1#1 39 gyffseigpi neivhiwafs slddraerra rlxadprwls flpkirdlie
TARGET ssssss sss ssssssss hhhhhhhhh hhh hhhh hhh sss
1vqs_1#1 ssssss sss sssssssss hhhhhhhhh hh hhhhh hhh sss
TARGET 481 HMESRIMIPL KISPL ---- ------- YE LRTYKLKPGT MIEWGNNW-A
1vqs_1#1 89 vaenkixkpa rfspl-xihh hhhhxf--ye irtyrlknga ipaylkvved
*
TARGET ssssssssss ss sssssss hhhhhh
1vqs_1#1 ssssssssss s ss sssssss hhhhhhhhh
TARGET 517 RAIKYRQEN- QEAVGGFFSQ IGELYVVHHL WAYKDLQSRE ETRNAAWRKR
1vqs_1#1 25 egieiqkshl gelvgyffse igpineivhi wafsslddra errarlxadp
TARGET sssssssss sssssssss ss hhhhh hhhhhhh
1vqs_1#1 hhhhhhhh sssssssss sssssssss sss hhhhh hhhhhhh
TARGET 566 GWDENVYYTV PLVRHMESRI MIPLKISPL ---------- YELRTYKLK
1vqs_1#1 75 rwlsflpkir dlievaenki xkparfspl- xhhhhhhxf- -yeirtyrlk
*
TARGET hhhhhhh sssssssss ssss sssssssss
1vqs_1#1 hhhhhhh sssssssss ssss s sssssssss
TARGET 604 PGTMIEWGNN W-ARAIKYRQ EN-QEAVGGF FSQIGELYVV HHLWAYKDLQ
1vqs_1#1 12 ngaipaylkv vedegieiqk shlgelvgyf fseigpinei vhiwafssld
TARGET hhhhhhh hhhhh ssssss sss ssssss sssss hh
1vqs_1#1 hhhhhhh hh hhhhh hhh ssssss sss ssssss ssssss hh
TARGET 652 SREETRNAAW RKRGWDENVY YTVPLVRHME SRIMIPLKIS PL -------
1vqs_1#1 62 draerrarlx adprwlsflp kirdlievae nkixkparfs pl-xihhhhh
TARGET hhhhhhhhhh hhhhhhh ssssss sssssss
1vqs_1#1 hhhhhhhhh hhhhhhhh ssssss sssssss
TARGET 694 ---- YELRT YKLKPGTMIE WGNNW-ARAI KYRQEN-QEA VGGFFSQIGE
1vqs_1#1 0 hxf--yeirt yrlkngaipa ylkvvedegi eiqkshlgel vgyffseigp
*
TARGET sssss ssss hhh hhh ss sssssss ss
1vqs_1#1 s sssss ssss hhh hhhhhh h hhhhhhh ss sssssss ss
TARGET 737 LYVVHHLWAY KDLQSREETR NAAWRKRGWD ENVYYTVPLV RHMESRIMIP
1vqs_1#1 48 ineivhiwaf sslddraerr arlxadprwl sflpkirdli evaenkixkp
TARGET sssssssss hhhhhhhh hhhh hhh hhhh ss ssssssssss
1vqs_1#1 ssssssssss hhhhhhhh hhhh hhh hhhh ss ssssssssss
TARGET 787 LKISPL
1vqs_1#1 98 arfsplx
TARGET s
1vqs_1#1 s
Template's ligands section
Ligands in the template:MPD : 4,SO4 : 8.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1vqs is annotated as OCTAMER
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: 1vqs.pdb1.gz
Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=OCTAMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.5 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1vqsA
Model was succesfully built as OCTAMER.
Template Selection
- Start SMR-Pipeline for:55895dd90c334818733cdd7c9e79cfb9 on BC2-cluster at Sat Feb 23 01:56:45
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
- 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 1vqsB (185-283) 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:55895dd90c334818733cdd7c9e79cfb9 on BC2-cluster at Sat Feb 23 02:02:33
2013
Template Search
no data available!
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.