SWISS-MODEL Repository - Model Details

Model Overview
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1
480

Sequence
UniProt P56475
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Neur_chan_LBD
Neur_chan_memb

Model 3D Structure
Model information:
Modelled residue range: 311 to 370
Based on template: [ 1vry ]  
Sequence Identity [%]: 60%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1vry): MONOMER
Model built: SINGLE CHAIN
Model: MONOMER

Ligand information: [details]
Ligands in the template: none.
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       VPARVPLG ITTVLTMSTI ITGVNASMPR VSYIKAVDIY LWVSFVFVFL
1vry_1#3  65533    lparvglg ittvltlttq ssgsraslpk vsyvkaidiw lavcllfvfs
                                                                      
TARGET              hhhhhh hhhhhhhhhh hh         hhhhhh   h hhhhhhhhhh
1vry_1#3            hhhhhh hhhhhhhhhh hh         hhhhhh   h hhhhhhhhhh


TARGET    49    SVLEYAAVNY LT                                         
1vry_1#3  45    alleyaavnf vsr                                        
                                                                      
TARGET          hhhhhhhhhh h                                          
1vry_1#3        hhhhhhhhhh h

Quality 


Template's ligands section 
Template without ligands. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 1vry is annotated as MONOMER 
 The template structure (1vry) was solved by NMR and does not contain any quaternary structure annotation 
 The template is annotated by the number of chains found in the PDB file 
      
 
Quaternary Structure Modelling of the Target Protein 
 The target and template sequences are too diverse (seqid: 60.000) to infer a conservation of the oligomeric state 
 Please use the advancend features of the SwissModel Project Mode 
       
 The target structure was calculated as SINGLE CHAIN 
 Model was succesfully built as MONOMER.

Template Selection 
 - Start SMR-Pipeline for:c35168c19a39d8ed32602dc78a7a3765 on BC2-cluster at Sat Feb 23 04:05:57
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...
FATAL - No templates found in HHSEARCH, strange
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with A found
 - No template with B found
 - No template with E found
 - No template with C found
 - No template with D found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O 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 1vryA (311-370) was successful 
 -               ************************************************
 - building model based on 3rhwE (85-369) 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:c35168c19a39d8ed32602dc78a7a3765 on BC2-cluster at Sat Feb 23 04:35:42
2013


Template Description
Match Chain SeqId

1vry: SECOND AND THIRD TRANSMEMBRANE DOMAINS OF THE ALPHA-1 SUBUNIT OF HUMAN GLYCINE RECEPTOR
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

311-370 1vryA 60%
[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.