SWISS-MODEL Repository - Model Details

Model Overview
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1
323

Sequence
UniProt A4FUQ5
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
7tm_1

Model 3D Structure
Model information:
Modelled residue range: 35 to 228
Based on template: [ 4dkl ]  
Sequence Identity [%]: 34%
Model date: 2013-02-17
Revision date: 2013-01-30

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

Ligand information: [details]
Ligands in the template: 1PE: 1, CL: 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                    ITFVLG VLGNGLVIWV -AGFQMAHTV TTVSYLNLAL
4dklA     65    mvtaitimal ys--ivcvvg lfgnflvmyv ivrytkmkta tniyifnlal
                                                                      
TARGET                          hhhhh hhhhhhhhhh  h       h hhhhhhhhhh
4dklA            hhhhhhhhh hh  hhhhhh hhhhhhhhhh hhh      h hhhhhhhhhh


TARGET    36    SDLSFMATLP LHIISMVMRG KWLFGWFLCK LVHIIANINL FVSIFLITLI
4dklA     113   adalatstlp fqsvnylm-g twpfgnilck ivisidyynm ftsiftlctm
                                                                      
TARGET          hhhhhhhhhh hhhhhhh          hhhh hhhhhhhhhh hhhhhhhhhh
4dklA           hhhhhhhhhh hhhhhhhh         hhhh hhhhhhhhhh hhhhhhhhhh


TARGET    86    AMDRCICVLC PVWSQNHRTV SLARKVVLGA WIFALLLTLP HFLFLTTVRD
4dklA     162   svdryiavch pvkaldfrtp rnakivnvcn wilssaiglp -vmfmattky
                                                                      
TARGET          hhhhhhhh    hhhhhh    hhhhhhhhhh hhhhhhhhhh hh      ss
4dklA           hhhhhhhh    hhhhhh    hhhhhhhhhh hhhhhhhhhh  hhhh     


TARGET    136   ARGDVYCISK FESWVATSEE QLKVSVIAAT ASGIINFIIG FSMPMSFIAI
4dklA     211   rqgsidctlt fshptwywen llkicv---- ------fifa fimpvliitv
                                                                      
TARGET          s  sss          hhhhh hhhhhsssss     sssss   hhhhhhhhh
4dklA                           hhhhh hhhhhh           hh    hhhhhhhhh


TARGET    186   CYGLMAAKI  ---------- ---------- ---------- ----------
4dklA     251   cyglmilrlk svrnifemlr ideglrlkiy kntegyytig ighlltksps
                                                                      
TARGET          hhhhhhhh                                              
4dklA           hhhhhhhh       hhhhhh hh       s ss   sss             


TARGET          ---------- ---------- ---------- ---------- ----------
4dklA     1039  lnaakseldk aigrntngvi tkdeaeklfn qdvdaavrgi lrnaklkpvy
                                                                      
TARGET                                                                
4dklA            hhhhhhhhh hh          hhhhhhhhh hhhhhhhhhh    hhhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
4dklA     1089  dsldavrraa linmvfqmge tgvagftnsl rmlqqkrwde aavnlaksrw
                                                                      
TARGET                                                                
4dklA           h   hhhhhh hhhhhh   h hhh   hhhh hhh   hhhh hhhhh   hh


TARGET          ---------- ---------- ---------- ---------- ----------
4dklA     1139  ynqtpnrakr vittfrtgtw dayekdrnlr ritrmvlvvv avfivcwtpi
                                                                      
TARGET                                                                
4dklA           hh   hhhhh hhhhhhh           hhh hhhhhhhhhh hhhhhhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
4dklA     297   hiyviikali tipettfqtv swhfcialgy tnsclnpvly afldenfkrc
                                                                      
TARGET                                                                
4dklA           hhhhhhh          hhhh hhhhhhhhhh hhhhhhhhhh h   hhhhhh


TARGET          ------                                                
4dklA     347   frefci                                                
                                                                      
TARGET                                                                
4dklA           hhhhh

Quality 


Template's ligands section 
Ligands in the template: 1PE: 1, CL: 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 
 4dkl 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: 4dkl.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 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:c33f674a21e52b297510746ddc2cb03b on BC2-cluster at Sun Feb 17 04:43:30
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 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 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 4dklA (35-228) was successful 
 -        ********************************************************************
 - building model based on 2lnlA (30-305) 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:c33f674a21e52b297510746ddc2cb03b on BC2-cluster at Sun Feb 17 04:47:44
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 ]  

23-315 2lnlA 28%
[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 ]  

22-172 3vw7A 26%
[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 ]  

26-306 4grvA 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.