SWISS-MODEL Repository - Model Details

Model Overview
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1
362

Sequence
UniProt P56485
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P56485: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
7tm_1

Model 3D Structure
Model information:
Modelled residue range: 248 to 318
Based on template: [ 3oe8 ]  
Sequence Identity [%]: 36%
Model date: 2014-09-19
Revision date: 2014-09-17

Quaternary structure information: [details]
Template (3oe8): TRIMER
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 ]

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                 



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
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 Fri Sep 19 14:22:03
2014 


 - 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 modified template library 
 - Summarize templates: 
 - No template with A found
 - No template with C 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 B found
 - No template with B found
 - No template with B 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
 - 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 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 Fri Sep 19 14:28:24
2014 




Template Description
Match Chain SeqId

4phu: CRYSTAL STRUCTURE OF HUMAN GPR40 BOUND TO ALLOSTERIC AGONI
Solved by: X-RAY, Resolution: 2.33A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

46-238 4phuA 18%
[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.




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