SWISS-MODEL Repository - Model Details

Model Overview
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1
423

Sequence
UniProt P32082
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
7tm_2
HRM

Model 3D Structure
Model information:
Modelled residue range: 34 to 121
Based on template: [ 2xdg ]  
Sequence Identity [%]: 77%
Model date: 2013-02-17
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2xdg): MONOMER
Model: MONOMER

Ligand information: [details]
Ligands in the template: EDO: 1, MG: 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        LRDDELA CLQAAEGTNN TSLGCPGTWD GLLCWPPTGS GQWVSLPCPE
2xdg_2#3  0     m--lredesa clqaaeempq ttlgcpatwd gllcwptags gewvtlpcpd
                                                                      
TARGET              hhhhhh hhhhhh            sss   sss       sssss    
2xdg_2#3           hhhhhhh hhhhhh            sss   sss       sssss    


TARGET    48    FFSHFGSDTG FVKRDCTITG WSNPFPPYPV ACPVPLELLT K         
2xdg_2#3  81    ffshfssesg avkrdctitg wsepfppypv acpvplella e-        
                                                                      
TARGET          hhh         ssssss  s ss     hhh h     hhh            
2xdg_2#3        hhh         ssssss  s ss     hhh h     hhh

Quality 


Template's ligands section 
Ligands in the template: EDO: 1, MG: 2. 
Ligands in the template that will be assessed: MG1, MG2. 
Model's ligands section 
MG1 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG1 will not be included in the final model. 
MG1: conservation:False, RMSD:False, included: False 
 
MG2 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG2 will not be included in the final model. 
MG2: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 2xdg 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: 2xdg.pdb3.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=MONOMER) 
 The corresponding reliability score is 0.526 (>0.5 indicates similarity) 
 Model was succesfully built as MONOMER.

Template Selection 
 - Start SMR-Pipeline for:b12c1c7d5a340fe078aa2e9b0e2cb131 on BC2-cluster at Sun Feb 17 17:12:32
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: 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
 - 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 2xdgB (34-121) was successful 
 -                           ***********************
 - building model based on 3vw7A (137-257) was successful 
 -                          **************************************************
 - building model based on 2lnlA (131-393) was not successful go to next best template
 - 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:b12c1c7d5a340fe078aa2e9b0e2cb131 on BC2-cluster at Sun Feb 17 17:14:39
2013


Template Description
Match Chain SeqId

2xdg: CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN GROWTH HORMONE RELEASING HORMONE RECEPTOR.
Solved by: X-RAY, Resolution: 1.95A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

34-121 2xdgA 77%
[Model]
34-121 2xdgB 77%
[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 ]  

137-257 3vw7A 13%
[Model]

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

131-393 2lnlA 13%
[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 ]  

137-256 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.