SWISS-MODEL Repository - Model Details

Model Overview
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1
368

Sequence
UniProt Q9FFY6
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9FFY6: 3702.AT5G13860.1

Domain
Link to: [ InterPro ]
UEV
Vps23_core

Model 3D Structure
Model information:
Modelled residue range: 34 to 160
Based on template: [ 1s1q ]  
Sequence Identity [%]: 38%
Model date: 2013-02-10
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1s1q): HETERO DIMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: CU: 1, SO4: 2.
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                       KSL IRQHLLNLIS SYTSLDPKTA TFTHNDGRSV
1s1qA     3     vsesqlkkxv skyky--rdl tvretvnvit lykdlkpvld syvfndgssr
                                                                      
TARGET                             hh hhhhhhhhhh h  sssssss ssss   sss
1s1qA             hhhhhhh         hhh hhhhhhhhhh h  sssssss ssss   sss


TARGET    34    ILLQADGTIP MPFQGVSYNI PVVIWLLESY PQYPPCVYVN PTRDMIIKRP
1s1qA     51    elxnltgtip vpyrgntyni piclwlldty pynppicfvk ptssxtik-t
                                                                      
TARGET          ssssssssss sss  sssss ssssss          sssss      sss  
1s1qA           ssssssssss sss  sssss ssssss          sssss      sss  


TARGET    84    HSNVSPSGLV SLPYLQNWIY PSSNLVDLAS HLSAAFSRDP PLYS      
1s1qA     100   gkhvdangki ylpylhewkh pqsdllgliq vxivvfgdep pvfs-     
                                                                      
TARGET            sss  sss s hhhh         hhhhhh hhhhhhhh   sss       
1s1qA             sss  sss s hhhh         hhhhhh hhhhhhhh   sss

Quality 


Template's ligands section 
Ligands in the template: CU: 1, SO4: 2. 
Ligands in the template that will be assessed: CU9002. 
Model's ligands section 
CU9002 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand CU9002 will not be included in the final model. 
CU9002: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 1s1q 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: 1s1q.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 1s1q_1

Template Selection 
 - Start SMR-Pipeline for:6032d75b86824c3c1a35ab37fd8f0b20 on BC2-cluster at Sat Feb  9 23:28:40
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with B found
 - No template with B found
 - No template with D found
 - No template with B found
 - No template with B found
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -        ****************************
 - building model based on 1s1qA (34-160) 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:6032d75b86824c3c1a35ab37fd8f0b20 on BC2-cluster at Sat Feb  9 23:53:19
2013


Template Description
Match Chain SeqId

4gpr: CRYSTAL STRUCTURE OF EHUBC5, A UBIQUITIN CONJUGATING ENZYMENTAMOEBA HISTOLYTICA
Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

36-154 4gprA 18%
[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.