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
3oe8A 27 pcnfnkiflp tiysiifltg ivgnglvilv mgyqkklrsm tdkyrlhlsv
3oe8A hhhhhh hhhhhhhhhh hhhhhhhhhh hhh h hhhhhhhhhh
3oe8A 83 adllfvitlp fwavdavanw yfgnflckav hviytvnlys svwilafisl
3oe8A hhhhh hh hhhhhhh hhhhhh hhhhhhhhhh hhhhhhhhhh
3oe8A 133 drylaivhat nsqrprklla ekvvyvgvwi pallltipdf ifanvseadd
3oe8A hhhhhhh hhhhhhh hhhhhhhhhh hhhh hhh hsssssss
3oe8A 183 ryicdrfypn dlwvvvfqfq himvglilpg ivilscycii isklshsgsn
3oe8A sssssss hhhhhhhhh hhhhhhhhhh hhhhhhhhhh
3oe8A 1003 ifemlrideg lrlkiykdte gyytigighl ltkspslnaa kseldkaigr
3oe8A hhhhhh ssssss ssss ss s hhhh hhhhhhhh
3oe8A 1053 ntngvitkde aeklfnqdvd aavrgilrna klkpvydsld avrraalinm
3oe8A sss hhh hhhhhhhhhh hhh hhhh h hhhhhhhhhh
3oe8A 1103 vfqmgetgva gftnslrmlq qkrwdeaavn laksrwynqt pnrakrvitt
3oe8A hhh hhhh hhhhhh hhhhhhhh hh hhh hhhhhhhhh
TARGET 1 HSSRKIIFS YVV---VFLV CWLPYHFVVL LDIFSILHYI
3oe8A 1153 frtgtwday- -hqkrkalkt tvililaffa cwlpyyigis idsfilleii
TARGET hhhhhhh hh hhhhhhhhhh hhhhhhh
3oe8A hhh hhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhh
TARGET 37 PFTCQLENVL FTALHVTQCL SLVHCCVNPV LYSFI
3oe8A 271 kqgcefentv hkwisiteal affhcclnpi lyafl-
TARGET hhhhhh hhhhhhhhhh hhhhhhhhhh hhhh
3oe8A hhhhhh hhhhhhhhhh h hhhhhh hhhh
Template's ligands section
Ligands in the template:ITD : 1.
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
3oe8 is annotated as TRIMER
PISA was used to annotate the quaternary structure, because the author assignment was not complete
The template was built based on the following PISA annotation file: 3oe8_assembly.xml.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 (=TRIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 3oe8C 3oe8B
Template Selection
- Start SMR-Pipeline for:696e426b6811da0f95cc7de9f48c8b68 on BC2-cluster at Sat Feb 23 02:20:24
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 A found
- No template with B found
- No template with G found
- No template with N found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with A found
- No template with C found
- No template with B found
- No template with I found
- No template with I found
- No template with I found
- No template with I found
- No template with B found
- No template with B found
- No template with B found
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:3): model based on new templates
- Send 3 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ****************
- building model based on 3oe8A (248-318) was successful
- ***************************************************************
- building model based on 2lnlA (45-328) was successful
- *********************************************************************
- building model based on 1l9hA (45-355) 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:696e426b6811da0f95cc7de9f48c8b68 on BC2-cluster at Sat Feb 23 02:25:50
2013
Template Search
| Template Description |
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2lnl: STRUCTURE OF HUMAN CXCR1 IN PHOSPHOLIPID BILAYERS Solved by: NMR, Identified by HHSEARCH |
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4grv: THE CRYSTAL STRUCTURE OF THE NEUROTENSIN RECEPTOR NTS1 IN NEUROTENSIN (8-13) Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH |
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3vw7: CRYSTAL STRUCTURE OF HUMAN PROTEASE-ACTIVATED RECEPTOR 1 (WITH ANTAGONIST VORAPAXAR AT 2.2 ANGSTROM Solved by: X-RAY, Resolution: 2.20A, 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.