SWISS-MODEL Repository - Model Details

Model Overview
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1
80

Sequence
UniProt Q21102
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q21102: 6239.K01H12.1

Domain
Link to: [ InterPro ]
zf-CSL

Model 3D Structure
Model information:
Modelled residue range: 1 to 70
Based on template: [ 2jr7 ]  
Sequence Identity [%]: 67%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2jr7): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ZN: 1.
Ligands in the model: ZN: 1
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       MSVFHDEV EIEDFEFDEE KDVYHYPCPC GDRFEIPREM LEMGEDVAQC
2jr7A     1       mavfhdev eiedfqyded setyfypcpc gdnfsitked lengedvatc
                                                                      
TARGET                 sss ss   sss    sssssss    ssssssshh hhh  sss  
2jr7A                  sss ss          sssssss    ssssssshh hhh  sss  


TARGET    49    PSCSLLIRVI YDPEDFVKLE TI ------- ------               
2jr7A     49    pscsliikvi ydkdqfvsge tvpapsanke lvkleh               
                                                                      
TARGET                ssss   hhhh                                     
2jr7A                 ssss   hhhh

Quality 


Template's ligands section 
Ligands in the template: ZN: 1. 
Ligands in the template that will be assessed: ZN85. 
Model's ligands section 
ZN85 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.050 
Given the properties calculated previously, the ligand A.ZN85 will be included in the final model. 
ZN85: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 2jr7 is annotated as MONOMER 
 The template structure (2jr7) 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 0.236 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:8389b24bdcb59c052c6682f0e026e0d7 on BC2-cluster at Thu Feb 21 03:55:00
2013 


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

FATAL - No A3m found

 - 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 2jr7A (1-70) 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:8389b24bdcb59c052c6682f0e026e0d7 on BC2-cluster at Thu Feb 21 03:55:51
2013


Template Description
Match Chain SeqId

2jr7: SOLUTION STRUCTURE OF HUMAN DESR1
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-70 2jr7A 67%
[Model]

1wge: SOLUTION STRUCTURE OF THE MOUSE DESR1
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-71 1wgeA 66%
[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.