SWISS-MODEL Repository - Model Details

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1
143

Sequence
UniProt Q9VVA0
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9VVA0: 7227.FBpp0075084

Domain
Link to: [ InterPro ]
CSD

Model 3D Structure
Model information:
Modelled residue range: 37 to 130
Based on template: [ 3aqq ]  
Sequence Identity [%]: 60%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3aqq): TETRAMER
Model built: SINGLE CHAIN

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         TRRTRT ASTSARALEN PVVTGMVKSF SRTKGHGFIT PNAGGEDVFC
3aqqB     43    lp--trrtrt fsatvrasqg pvykgvckcf crskghgfit padggpdifl
                                                                      
TARGET                     hhhhhhhhh    ssssss       ssssss ss     sss
3aqqB                      hhhhhhhhh    ssssss       ssssss ss     sss


TARGET    47    HVSDIEGEYV PMPGDEVKYR LCAIPPKYEK HQAVHVQISH LTPEVHHK -
3aqqB     91    hisdvegeyv pvegdevtyk mcsippknek lqavevvith lapgtkhetw
                                                                      
TARGET          ss             ssssss ssss     s ssss  sss            
3aqqB           ss             ssssss ssss     s ssss  sss            


TARGET          -                                                     
3aqqB     141   s                                                     
                                                                      
TARGET                                                                
3aqqB

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3aqq is annotated as TETRAMER 
 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: 3aqq.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Not all chains of the complex were                      identified 
 Please use the advancend features of the SwissModel Project Mode 
   
 The target structure was calculated as SINGLE CHAIN

Template Selection 
 - Start SMR-Pipeline for:f5223db465788751542e616517373054 on BC2-cluster at Thu Feb 21 20:34:10
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

FATAL - No A3m found

 - No template with A found
 - No template with C found
 - No template with D found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                      *****************************************************
 - building model based on 3aqqB (37-130) 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:f5223db465788751542e616517373054 on BC2-cluster at Thu Feb 21 20:34:39
2013


Template Description
Match Chain SeqId

3aqq: CRYSTAL STRUCTURE OF HUMAN CRHSP-24
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

37-130 3aqqB 61%
[Model]
37-130 3aqqD 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.