SWISS-MODEL Repository - Model Details

Model Overview
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1
112

Sequence
UniProt Q9D1C3
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9D1C3: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
Trm112p

Model 3D Structure
Model information:
Modelled residue range: 47 to 93
Based on template: [ 2jny ]  
Sequence Identity [%]: 51%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2jny): MONOMER
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        TFHPALL QFLVCPLSKK PLRYEASTNE LVNEELGIAY PIIDGIPNMI
2jnyA     1     m--sldpqll evlacpkdkg plryleseql lvnerlnlay riddgipvll
                                                                      
TARGET                       sss    s sssss   ss sss    sss sss  sss  
2jnyA                        sss    s sssss   ss sss    sss sss  sss  


TARGET           --------- ---                                        
2jnyA     49    ideatewtpn nle                                        
                                                                      
TARGET                                                                
2jnyA

Quality 


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

 
Quaternary Structure Annotation of the Template 
 2jny is annotated as MONOMER 
 The template structure (2jny) 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 
 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 (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.334 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:f0cb7decc27ea512aaa46f72ae769e86 on BC2-cluster at Fri Feb 22 19:15:29
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - 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 2jnyA (47-93) 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:f0cb7decc27ea512aaa46f72ae769e86 on BC2-cluster at Fri Feb 22 19:16:26
2013

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.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.