SWISS-MODEL Repository - Model Details

Model Overview
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1
204

Sequence
UniProt Q9BRP8
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9BRP8: 9606.ENSP0000038

Domain
Link to: [ InterPro ]
Mago-bind

Model 3D Structure
Model information:
Modelled residue range: 7 to 38
Based on template: [ 1rk8 ]  
Sequence Identity [%]: 62%
Model date: 2012-10-26
Revision date: 2012-10-15

Quaternary structure information: [details]
Template (1rk8): HETERO TRIMER
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 2012-10-15. 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      PAATETGKY IASTQRPDGT WRKQRRVKEG YVP                  
1rk8C     3     tylqssegkf ipatkrpdgt wrkarrvkdg yvp-                 
                                                                      
TARGET            sss  sss s  sss   s ss  sss                         
1rk8C             sss  sss s  sss   s ss  sss

Quality 


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

 
Quaternary Structure Annotation of the Template 
 1rk8 is annotated as HETERO TRIMER 
 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: 1rk8.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 1rk8_1 is labeled HETERO oligomeric, i.e the sequences of the chains are not identical 
 Modeling of hetero oligomers is not yet supported by the SWISS-MODEL automated modeling pipeline 
 Please use the advancend features of the SwissModel Project Mode 
       
 The final model was calculated as single chain

Template Selection 
 - Start SMR-Pipeline for:6f50d040d4daef4d1a66d16d53801ac0 on BC2-cluster at Fri Oct 26 08:57:44
2012 


 - 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: 
 - Skip Template HHsearch issue
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Selected template(s): no changes compared to previous version of the Repository:
 -  Template: 1rk8C (7-38) Sequence Identity: 62.500
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -    *************
 - building model based on 1rk8C (7-38) 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:6f50d040d4daef4d1a66d16d53801ac0 on BC2-cluster at Fri Oct 26 09:02:57
2012

no data available!
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.
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