SWISS-MODEL Repository - Model Details

Model Overview
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1
132

Sequence
UniProt P09468
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
ATP-synt_DE
ATP-synt_DE_N

Model 3D Structure
Model information:
Modelled residue range: 1 to 132
Based on template: [ 2rq7 ]  
Sequence Identity [%]: 62%
Model date: 2013-05-04
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (2rq7): 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 ]

Alignment 

TARGET    1       MTLNLCVL TPNRIVWDSE VKEIILSTNS GQIGVLANHA PIATAVDIGI
2rq7A     1       mvmtvrvi apdktvwdap aeevilpstt gqlgilsnha plltaletgv
                                                                      
TARGET              ssssss s  sssssss s ssssss   sssss       sssss  ss
2rq7A               ssssss s  sssssss s ssssss   sssss       sssss  ss


TARGET    49    LKIRLANQWL TMALMGGFAR IGNNEITILV NDAEKNSDID PQEAQQTLEI
2rq7A     49    mrvrqdrewv aialmggfae vennevtilv ngaergdtid pqeaqqtlei
                                                                      
TARGET          ssss     s ssssssssss ss sssssss ssss        hhhhhhhhh
2rq7A           ssss     s ssssssssss ss sssssss ssss        hhhhhhhhh


TARGET    99    AEANLRKAEG KRQTIEANLA LRRARTRVEA LNTI -               
2rq7A     99    aeanlrkaeg arqkieanla lrrartrvea sntiss               
                                                                      
TARGET          hhhhh       hhhhhhhhh hhhhhhhhhh h                    
2rq7A           hhhhh       hhhhhhhhh hhhhhhhhhh h

Quality 


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

 
Quaternary Structure Annotation of the Template 
 2rq7 is annotated as MONOMER 
 The template structure (2rq7) 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 0.332 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:4b2c32a6420128a7e038661f5b5a287b on BC2-cluster at Sat May  4 00:50:24
2013 


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

 - 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 2rq7A (1-132) 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:4b2c32a6420128a7e038661f5b5a287b on BC2-cluster at Sat May  4 00:51:36
2013


Template Description
Match Chain SeqId

2rq7: SOLUTION STRUCTURE OF THE EPSILON SUBUNIT CHIMERA COMBININTHE N-TERMINAL BETA-SANDWICH DOMAIN FROM T. ELONGATUS BP-F1 AND THE C-TERMINAL ALPHA-HELICAL DOMAIN FROM SPINACH CHLOROPLAST F1
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-132 2rq7A 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.