SWISS-MODEL Repository - Model Details

Model Overview
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1
264

Sequence
UniProt Q682V0
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q682V0: 3702.AT3G23100.1

Domain
Link to: [ InterPro ]
XRCC4

Model 3D Structure
Model information:
Modelled residue range: 39 to 213
Based on template: [ 3ii6 ]  
Sequence Identity [%]: 25%
Model date: 2013-02-19
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3ii6): HETERO TRIMER
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 ]

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                           FVKGTWHNS- --RFDISVTD GSSSWICNAT
3ii6C     1     merkisrihl vsepsith-- flqvswektl esgfvitltd ghsawtgtvs
                                                                      
TARGET                                sssss         ssssss      sssss 
3ii6C            sssssss          s   ssssss        ssssss     ssssss 


TARGET    28    EEEVAERAAQ WDQPVSEYL- KLAEQYLGFQ QPNSVYSFSD ALEGSKRLSW
3ii6C     49    eseisqeadd memekgkyvg elrkallsga gpadvytfnf skesc---yf
                                                                      
TARGET          hhhhhhhhhh h      h     hhhh         ssssss s       ss
3ii6C           hhhhhhhhhh h     hhhh hhhhhh         ssssss s       ss


TARGET    77    TFEKEGTKLE WRWKCKPSDD -------SKK ITVGILDFLM E---ANIRLS
3ii6C     96    ffeknlkdvs frlgsfnlek venpaevire licycldtta enqaknehlq
                                                                      
TARGET          ssssss  ss ssssss                    hhhhh        hhhh
3ii6C           ssssss  ss ssssss  ss s   hhhhhh    hhhhhhh hhhhhhhhhh


TARGET    117   EEVVNKTRSF EKMRSEAERC LAQGEKLCDE KTEFESATYA KFLSVLNAKK
3ii6C     146   kenerllrdw ndvqgrfekc vsakeal--- ----etdlyk rfilvlnekk
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh hhhhh           hhhhh hhhhhhhhhh
3ii6C           hhhhhhhhhh hhhhhhhhhh hhhh           hhhhhh hhhhhhhhhh


TARGET    167   AKLRALRDK  ---                                        
3ii6C     189   tkirslhnkl lna                                        
                                                                      
TARGET          hhhhhhhhh                                             
3ii6C           hhhhhhhhhh h

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3ii6 is annotated as HETERO TRIMER 
 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: 3ii6.pdb2.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3ii6_2

Template Selection 
 - Start SMR-Pipeline for:480ca218b08db0163e35119f51ba6327 on BC2-cluster at Tue Feb 19 17:31:05
2013 


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

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with D found
 - No template with Y found
 - No template with B found
 - No template with X found
 - Warning: Oligomer Prediction was not successfull!

 - 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 3ii6C (39-213) 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:480ca218b08db0163e35119f51ba6327 on BC2-cluster at Tue Feb 19 17:32:03
2013

no data available!
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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