SWISS-MODEL Repository - Model Details

Model Overview
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1
593

Sequence
UniProt Q8WXI9
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q8WXI9: 9606.ENSP0000035

Domain
Link to: [ InterPro ]
GATA

Model 3D Structure
Model information:
Modelled residue range: 160 to 199
Based on template: [ 2l2l ]  
Sequence Identity [%]: 75%
Model date: 2014-10-08
Revision date: 2014-10-06

Quaternary structure information: [details]
Template (2l2l): HETERO DIMER
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 ]

Alignment

TARGET    1          EERQQ LIKQLRDELR LEEARLVLLK KLRQSQLQKE NVVQK     
2l2lA     136   gsp--eerer mikqlkeelr leeaklvllk klrqsqiqke ataqk-    
                                                                      
TARGET                hhhh hhhhhhhhhh hhhhhhhhhh hhhhhh               
2l2lA                hhhhh hhhhhhhhhh hhhhhhhhhh hhhhhh               



Quality


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


Quaternary Structure Annotation of the Template
2l2l is annotated as HETERO DIMER
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: 2l2l.pdb1.gz

Quaternary Structure Modelling of the Target Protein
2l2l_1


Template Selection
 - Start SMR-Pipeline for:f750b9f9d3b6fdc62aaabf85083f4f18 on BC2-cluster at Wed Oct  8 15:28:45
2014 


 - 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

 - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - No template with B found
 - No template with B found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                       *****
 - building model based on 2l2lA (160-199) was successful 
 -                                                         ****
 - building model based on 2vusM (417-446) 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:f750b9f9d3b6fdc62aaabf85083f4f18 on BC2-cluster at Wed Oct  8 15:29:26
2014 




Template Description
Match Chain SeqId

2l2l: SOLUTION STRUCTURE OF THE COILED-COIL COMPLEX BETWEEN MBD2P66ALPHA
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

160-199 2l2lA 75%
[Model]

2vut: CRYSTAL STRUCTURE OF NAD-BOUND NMRA-AREA ZINC FINGER COMPLEX
Solved by: X-RAY, Resolution: 2.8A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

419-446 2vutK 36%
[Model]
419-446 2vutL 36%
[Model]
419-446 2vutM 36%
[Model]
419-446 2vutN 36%
[Model]
419-446 2vutO 36%
[Model]
419-446 2vutP 36%
[Model]
419-446 2vutI 36%
[Model]
419-446 2vutJ 36%
[Model]

2vuu: CRYSTAL STRUCTURE OF NADP-BOUND NMRA-AREA ZINC FINGER COMPLEX
Solved by: X-RAY, Resolution: 2.8A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

419-446 2vuuK 36%
[Model]
419-446 2vuuL 36%
[Model]
419-446 2vuuM 36%
[Model]
419-446 2vuuN 36%
[Model]
419-446 2vuuO 36%
[Model]
419-446 2vuuP 36%
[Model]
419-446 2vuuI 36%
[Model]
419-446 2vuuJ 36%
[Model]

2vus: CRYSTAL STRUCTURE OF UNLIGANDED NMRA-AREA ZINC FINGER COMPLEX
Solved by: X-RAY, Resolution: 2.8A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

419-446 2vusK 36%
[Model]
419-446 2vusL 36%
[Model]
419-446 2vusN 36%
[Model]
419-446 2vusO 36%
[Model]
419-446 2vusP 36%
[Model]
419-446 2vusI 36%
[Model]
419-446 2vusJ 36%
[Model]
417-446 2vusM 37%
[Model]

7gat: SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATSITE, 34 STRUCTURES
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

415-446 7gatA 34%
[Model]

6gat: SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATSITE, REGULARIZED MEAN STRUCTURE
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

415-446 6gatA 34%
[Model]

5gat: SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAINOF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, 35 STRUCTURES
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

414-446 5gatA 33%
[Model]

4gat: SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAINOF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

414-446 4gatA 33%
[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.




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