SWISS-MODEL Repository - Model Details

Model Overview
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1
318

Sequence
UniProt P32453
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P32453: 4932.YNL315C

Domain
Link to: [ InterPro ]
ATP11

Model 3D Structure
Model information:
Modelled residue range: 119 to 318
Based on template: [ 2p4f ]  
Sequence Identity [%]: 61%
Model date: 2013-02-19
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2p4f): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: P6G: 1.
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        PFKTLDS FLDVGKLKDL SKQEVEFLWR ARWAQKDNTL CAVIPV-SVY
2p4fA     94    kdkpyktldd ylkldkikdl skqeveflwr akwsnrddsl vavvpyvktf
                                                                      
TARGET                  hh    hh       hhhhhhhhh hhh    sss ssss      
2p4fA                   hh    hh       hhhhhhhhh hhh    sss ssssss    


TARGET    47    DKMMANARNN PIFVLPLPRQ VQSEDAKPNE EQGMELHYIQ WQFVGPQTTH
2p4fA     144   qgmykyavkn plfvlplprp v--------- ----elqyvq wqfagpntvh
                                                                      
TARGET          hhhhhhhhh  ssssssssss sss     ss ssssssssss ssss  ssss
2p4fA           hhhhhhhhh  sssssss                   ssssss ssss  ssss


TARGET    97    CMMTSLAEYK LHQEFARPHT TLQFHSDLVK DKGIVFMNGH VEPDTNVNVQ
2p4fA     195   clitslaeyk lhqdfakpht tiqfhldlan dkdmvlmngq vesdsnvslq
                                                                      
TARGET          ssssss       hhh   ss ssssss         ssssss ss      hh
2p4fA           ssssss   h    hh   ss ssssss   h h ssssssss ss      hh


TARGET    147   DAQLLLLNVQ RFYGAMGEET PVAKQRVQLL RDFSKASPGF TVEKLISLSQ
2p4fA     245   daqllllnvq rfygamgset siakeriqll edfnkgsqnf dinkliqlaq
                                                                      
TARGET          hhhhhhhhhh hh         hhhhhhhhhh hhhhh       hhhhhhhhh
2p4fA           hhhhhhhhhh hh         hhhhhhhhhh hhhhh       hhhhhhhhh


TARGET    197   SMEN                                                  
2p4fA     295   smen-                                                 
                                                                      
TARGET                                                                
2p4fA

Quality 


Template's ligands section 
Ligands in the template: P6G: 1. 
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 2p4f is annotated as MONOMER 
 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: 2p4f.pdb1.gz 
      
 
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 0.146 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:4ac83aa754f99c2b2b964ce2fd9837f1 on BC2-cluster at Mon Feb 18 23:28:29
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:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                               **************************************************
 - building model based on 2p4fA (119-318) 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:4ac83aa754f99c2b2b964ce2fd9837f1 on BC2-cluster at Mon Feb 18 23:29:47
2013


Template Description
Match Chain SeqId

2p4f: CRYSTAL STRUCTURE OF ATP11 FUNCTIONAL DOMAIN FROM CANDIDA GLABRATA
Solved by: X-RAY, Resolution: 1.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

119-318 2p4fA 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.