SWISS-MODEL Repository - Model Details

Model Overview
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1
322

Sequence
UniProt Q9R0M1
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9R0M1: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
7tm_1

Model 3D Structure
Model information:
Modelled residue range: 33 to 152
Based on template: [ 4djh ]  
Sequence Identity [%]: 36%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (4djh): DIMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: JDC: 1, OLC: 2, PEG: 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                  LYSLVFLL SLVGNSLVLW VLVKYENLES LTNIFILNLC
4djhB     55    spaipviita --vysvvfvv glvgnslvmf viirytkmkt atniyifnla
                                                                      
TARGET                        hhhhhhh hhhhhhhhhh hhhh       hhhhhhhhhh
4djhB             hhhhhhhh   hhhhhhhh hhhhhhhhhh hhhh       hhhhhhhhhh


TARGET    39    LSDLMFSCLL PV--LISAQW SWFLGDFFCK FFNMIFGISL YSSIFFLTIM
4djhB     103   ladalvtttm pfqstvylmn swpfgdvlck ivlsidyynm ftsiftltmm
                                                                      
TARGET          hhhhhhhhh                  hhhhh hhhhhhhhhh hhhhhhhhhh
4djhB           hhhhhhhhhh hhhhhhhhh       hhhhh hhhhhhhhhh hhhhhhhhhh


TARGET    87    TIHRYLSVVS PISTLGIHTL RCRVLVTSCV WAAS ----- ----------
4djhB     153   svdryiavch pvkaldfrtp lkakiinici wllsssvgis aivlggtkvr
                                                                      
TARGET          hhhhhhhh    hhhhh   h hhhhhhhhhh hhhh                 
4djhB           hhhhhhh    hhhhhh   h hhhhhhhhhh hhhhhhhhhh hhhsssssss


TARGET          ---------- ---------- ---------- ---------- ----------
4djhB     203   edvdviecsl qfpdddysww dlfmkicvfi fafvipvlii ivcytlmilr
                                                                      
TARGET                                                                
4djhB               ssssss s     hhhh hhhhhhhhhh    hhhhhhh hhhhhhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
4djhB     253   lksvrllsgn ifemlrideg lrlkiykdte gyytigighl ltkspslnaa
                                                                      
TARGET                                                                
4djhB           hhhh       hhhhhhhhh    ssssss    ssss   ss s      hhh


TARGET          ---------- ---------- ---------- ---------- ----------
4djhB     1043  kseldkaigr ntngvitkde aeklfnqdvd aavrgilrna klkpvydsld
                                                                      
TARGET                                                                
4djhB           hhhhh         sss hhh hhhhhhhhhh hhhhhhh    hhhhhhh   


TARGET          ---------- ---------- ---------- ---------- ----------
4djhB     1093  avrraalinm vfqmgetgva gftnslrmlq qkrwdeaavn laksrwynqt
                                                                      
TARGET                                                                
4djhB           hhhhhhhhhh hh   hhh    hhhhhhhh    hhhhhhhh hh   hhh  


TARGET          ---------- ---------- ---------- ---------- ----------
4djhB     1143  pnrakrvitt frtgtwdayr ekdrnlrrit rlvlvvvavf vvcwtpihif
                                                                      
TARGET                                                                
4djhB            hhhhhhhhh hhh               hhh hhhhhhhhhh hh   hhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
4djhB     294   ilvealgsta alssyyfcia lgytnsslnp ilyafldenf krcfrdfcfp
                                                                      
TARGET                                                                
4djhB           hhhhhh       hhhhhhhh hhhhhhhhhh hhhh   hhh hhhhhhhh

Quality 


Template's ligands section 
Ligands in the template: JDC: 1, OLC: 2, PEG: 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 
 4djh is annotated as DIMER 
 PISA was used to annotate the quaternary structure, because the author assignment was not complete  
  A biological unit file could be identified with the same complex description as the PISA annotation and was used to build the assembly: 4djh.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 0.184 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 4djhA

Template Selection 
 - Start SMR-Pipeline for:b550d3230dd38c2cf58eba8b98633150 on BC2-cluster at Fri Feb 22 17:16:52
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 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 A 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 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
 - 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 4djhB (33-152) was successful 
 -                                                    ********************
 - building model based on 3oe6A (206-287) was successful 
 -         ****************************************************************
 - building model based on 2lnlA (31-287) 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:b550d3230dd38c2cf58eba8b98633150 on BC2-cluster at Fri Feb 22 17:20:46
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 ]  

17-297 2lnlA 31%
[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 ]  

25-285 3vw7A 14%
[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 ]  

24-288 4grvA 13%
[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.