SWISS-MODEL Repository - Model Details

Model Overview
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1
456

Sequence
UniProt Q8TA83
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q8TA83: 6239.F22B7.5a.1

Domain
Link to: [ InterPro ]
DnaJ
DnaJ_CXXCXGXG
DnaJ_C

Model 3D Structure
Model information:
Modelled residue range: 41 to 110
Based on template: [ 2dn9 ]  
Sequence Identity [%]: 61%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2dn9): MONOMER
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           SKED YYKTLGVDKK SDAKAIKKAY FQLAKKYHPD VNKTK-EAQT
2dn9_1#4  1     gssg--ssgd yyqilgvprn asqkeikkay yqlakkyhpd tnkddpkake
                                                                      
TARGET                     hhhhh        hhhhhhhh hhhhhh             hh
2dn9_1#4                   hhhhh        hhhhhhhh hhhhhh           hhhh


TARGET    44    KFQEISEAYE VLSDDTKRQE YDAYGSG -- -                    
2dn9_1#4  49    kfsqlaeaye vlsdevkrkq ydaygsgpss g                    
                                                                      
TARGET          hhhhhhhhhh hh   hhhhh hhh                             
2dn9_1#4        hhhhhhhhhh hh   hhhhh hhh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 2dn9 is annotated as MONOMER 
 The template structure (2dn9) 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 quaternary structure can be assumed to be identical 
 Model was succesfully built as MONOMER.

Template Selection 
 - Start SMR-Pipeline for:361fe91d7c3e43c102dacc75d4727278 on BC2-cluster at Thu Feb 21 00:13:01
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
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:4): model based on new templates
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -        ************
 - building model based on 2dn9A (41-110) was successful 
 -                                *************
 - building model based on 1exkA (178-253) was successful 
 -                               *********************************
 - building model based on 1nltA (171-357) was successful 
 -         ***************************
 - building model based on 3apqB (43-194) 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:361fe91d7c3e43c102dacc75d4727278 on BC2-cluster at Thu Feb 21 00:15:16
2013


Template Description
Match Chain SeqId

2dn9: SOLUTION STRUCTURE OF J-DOMAIN FROM THE DNAJ HOMOLOG, HUMATID1 PROTEIN
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

41-110 2dn9A 62%
[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.