SWISS-MODEL Repository - Model Details

Model Overview
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1
378

Sequence
UniProt P47774
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
7tm_1

Model 3D Structure
Model information:
Modelled residue range: 54 to 250
Based on template: [ 3oe9 ]  
Sequence Identity [%]: 40%
Model date: 2013-02-15
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3oe9): DIMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ITD: 1.
Ligands in the model: none.
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 ]



Alignment 

TARGET    1         RNFKAW FLPLMYSVIC FVGLLGNGLV ILTYIYFKRL KTMTDTYLLN
3oe9A     28    cf--rnfnki flptiysiif ltgivgnglv ilvmgyqkkl rsmtdkyrlh
                                                                      
TARGET                        hhhhhhh hhhhhhhhhh hhhh          hhhhhhh
3oe9A                       hhhhhhhhh hhhhhhhhhh hhhhh         hhhhhhh


TARGET    47    LAVADILFLL ILPFWAYSEA KSWIFGVYLC KGIFGIYKLS FFSGMLLLLC
3oe9A     80    lsvadllfvi tlpfwavdav anwyfgnflc kavhviytvn lyssvwilaf
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh       hhhh hhhhhhhhhh hhhhhhhhhh
3oe9A           hhhhhhhhhh hhhhhhhhhh       hhhh hhhhhhhhhh hhhhhhhhhh


TARGET    97    ISIDRYVAIV QAVSAHRHRA RVLLISKLSC VGIWMLALFL SIPELLYSGL
3oe9A     130   isldrylaiv hatnsqrprk --llaekvvy vgvwipalll tipdfifanv
                                                                      
TARGET          hhhhhhhhhh                    h    hhhhhhhh hhhh  ssss
3oe9A           hhhhhhhhh          hh   hhh   h    hhhhhh    hhh  ssss


TARGET    147   QKNSGEDTLR CSLVSAQVEA LITIQVAQMV FGFLVPMLAM SFCYLIIIRT
3oe9A     178   se--addryi cdrfypndlw vvvfqfqhim vglilpgivi lscyciiisk
                                                                      
TARGET          s        s ssss    hh hhh   hhhh h   hhhhhh hhhhhhhhhh
3oe9A           s        s ssss    hh hhh   hhhh h   hhhhhh hhhhhhhhhh


TARGET    197   L -------- ---------- ---------- ---------- ----------
3oe9A     226   lshnifemlr ideglrlkiy kgyytigigh lltkspslna akseldkaig
                                                                      
TARGET                                                                
3oe9A              hhhhhhh hhh   sss     sss   s ss     hhh hhhhhh    


TARGET          ---------- ---------- ---------- ---------- ----------
3oe9A     1052  rntngvitkd eaeklfnqdv daavrgilrn aklkpvydsl davrraalin
                                                                      
TARGET                                                                
3oe9A               sss hh hhhhhhhhhh hhhhhh   h hhhhhhhh    hhhhhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
3oe9A     1102  mvfqmgetgv agftnslrml qqkrwdeaav nlaksrwynq tpnrakrvit
                                                                      
TARGET                                                                
3oe9A           hhh   hhhh h   hhhhhh    hhhhhhh hh    h    hhhhhhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
3oe9A     1152  tfrtgtwday kalkptvili laffacwlpy yigisidsfi lleiikcefe
                                                                      
TARGET                                                                
3oe9A           hhhh          hhhhhhh hhhhhhhhhh hhhhhhhhhh h      hhh


TARGET          ---------- ---------- ------                          
3oe9A     278   ntvhkwisit ealaffhccl npilya                          
                                                                      
TARGET                                                                
3oe9A           hhhhhhhhhh hhhhhhh    hhh

Quality 


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 
 3oe9 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: 3oe9.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 (=DIMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.004 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 3oe9B

Template Selection 
 - Start SMR-Pipeline for:c45dd7e71693b788cb938da5aabe8195 on BC2-cluster at Fri Feb 15 19:18:12
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

FATAL - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - 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 B found
 - No template with G found
 - No template with N 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
 - 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:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -            ******************************************
 - building model based on 3oe9A (54-250) was successful 
 -            *************************************************************
 - building model based on 2lnlA (52-341) 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:c45dd7e71693b788cb938da5aabe8195 on BC2-cluster at Fri Feb 15 19:23:04
2013


Template Description
Match Chain SeqId

2lnl: STRUCTURE OF HUMAN CXCR1 IN PHOSPHOLIPID BILAYERS
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

54-345 2lnlA 37%
[Model]

4grv: THE CRYSTAL STRUCTURE OF THE NEUROTENSIN RECEPTOR NTS1 IN NEUROTENSIN (8-13)
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

57-335 4grvA 16%
[Model]

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
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

56-332 3vw7A 16%
[Model]

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.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.