SWISS-MODEL Repository - Model Details

Model Overview
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1
393

Sequence
UniProt P21761
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
7tm_1

Model 3D Structure
Model information:
Modelled residue range: 27 to 153
Based on template: [ 4eiy ]  
Sequence Identity [%]: 35%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (4eiy): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: PEG: 2.
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                 VTILLVVII CGLGIVGNIM VVLVVMRTKH MRTPTNCYLV
4eiyA     65535  gappimgss- -vyitvelai avlailgnvl vcwavwlnsn lqnvtnyfvv
                                                                      
TARGET                       hhhhhhhh hhhhhhhhhh hhhhhhh       hhhhhhh
4eiyA               hhhhh   hhhhhhhhh hhhhhhhhhh hhhhhhh       hhhhhhh


TARGET    40    SLAVADLMVL VAAGLPNITD SIYGSWVYGY VGCLCITYLQ YLGINASSCS
4eiyA     47    slaaadiavg vlaipfait- -istgfcaac hgclfiacfv lvltqssifs
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhh           h hhhhhhhhhh hhhhhhhhhh
4eiyA           hhhhhhhhhh    hhhhhh   hh  sssss hhhhhhhhhh hhhhhhhhhh


TARGET    90    ITAFTIERYI AICHPIKAQF LCTFSRAKKI IIFVWAFT - ----------
4eiyA     95    llaiaidryi airiplryng lvtgtrakgi iaicwvlsfa igltpmlgwn
                                                                      
TARGET          hhhhhhhhhh hh      hh    hhhhhhh hhhhhhhh             
4eiyA           hhhhhhhhhh hh      hh    hhhhhhh hhhhhhhhhh h   hh    


TARGET          ---------- ---------- ---------- ---------- ----------
4eiyA     145   ncgqpkegkn hsqgcgegqv aclfedvvpm nymvyfnffa cvlvplllml
                                                                      
TARGET                                                                
4eiyA                 hhhh hhh    sss ss       h hhhhhhhhhh hhhhhhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
4eiyA     195   gvylriflaa rrqladledn wetlndnlkv iekadnaaqv kdaltkmraa
                                                                      
TARGET                                                                
4eiyA           hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hh    hhhh hhhhhhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
4eiyA     1037  aldaqkmkdf rhgfdilvgq iddalklane gkvkeaqaaa eqlkttrnay
                                                                      
TARGET                                                                
4eiyA           hhhh   hhh hhhhhhhhhh hhhhhhhh    hhhhhhhhh hhhhhhhh  


TARGET          ---------- ---------- ---------- ---------- ----------
4eiyA     1102  iqkylerars tlqkevhaak slaiivglfa lcwlplhiin cftffcpdcs
                                                                      
TARGET                                                                
4eiyA            hhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhh     


TARGET          ---------- ---------- ---------- ---------- ----      
4eiyA     264   haplwlmyla ivlshtnsvv npfiyayrir efrqtfrkii rshv      
                                                                      
TARGET                                                                
4eiyA              hhhhhhh hhhhhh   h hhhhhhh    hhhhhhhhhh hhh

Quality 


Template's ligands section 
Ligands in the template: PEG: 2. 
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 
 4eiy is annotated as MONOMER 
 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: 4eiy.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 (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.388 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:3121e1f5f20cba55fda14101f8c11a3c on BC2-cluster at Fri Feb 22 22:26:37
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 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 C found
 - No template with B found
 - No template with B found
 - No template with L found
 - No template with H found
 - No template with B found
 - No template with B found
 - No template with L found
 - No template with H 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 C found
 - No template with B found
 - No template with C found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:4): model based on new templates
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -      **************************
 - building model based on 4eiyA (27-153) was successful 
 -                                                       **************
 - building model based on 4dajA (266-332) was successful 
 -      **************************************
 - building model based on 4djhB (26-211) was successful 
 -      *****************************************************************
 - building model based on 2ydvA (27-346) 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:3121e1f5f20cba55fda14101f8c11a3c on BC2-cluster at Fri Feb 22 22:31:42
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 ]  

24-338 2lnlA 18%
[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 ]  

22-329 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 ]  

21-326 3vw7A 12%
[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.