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Model Overview
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1
402

Sequence
UniProt Q09524
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q09524: 6239.E02H1.3.2

Domain
Link to: [ InterPro ]
PseudoU_synth_1
PseudoU_synth_1

Model 3D Structure
Model information:
Modelled residue range: 82 to 273
Based on template: [ 1vs3 ]  
Sequence Identity [%]: 25%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1vs3): 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 ]

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 

                                                       
1vs3A     1     mrrllllcey dgtlfaglqr qgrglrtvqg eleralpgig alpkavaa--
                                                                      
                                                       
1vs3A            sssssssss s                 hhh hhhhhhh  s ss   sss  


TARGET    1     GRTDKGVSAF KQTAAMVVRS LCPGDSGVFW SDSTQEHQKV DYKASGEELP
1vs3A     49    grtdagvhal ampfhvdves aipv------ ---------- ------ekvp
                                                                      
TARGET                                     hhhhh h               hhhhh
1vs3A                  sss  ssssssss                              hhhh


TARGET    51    YVKMLNGVLP KTIRVFAWAP VAQTFNARFD CNRRTYKYSF ----------
1vs3A     77    --ealnrllp edlkvvgare vapdfharkd alwrayryri lvrphpspll
                                                                      
TARGET             hhhhh                    hhh     sssssss           
1vs3A             hhhhhh    sssssssss s     hhh    ssssssss sss       


TARGET    91    ------AKAD LNLEKMRQGA ELLVGEHDFS NFCQIDMNE- -KRLLQSYVR
1vs3A     125   rhralwvrrp ldleameeal slllgrhnfl gfakeetrpg erellearl-
                                                                      
TARGET                       hhhhhhhh hh  sss                sss      
1vs3A               sss      hhhhhhhh hh  sssssh h        s ssss ssss 


TARGET    133   KVYEVKVEQV STHPENDMYS MVELTVSGSG FLWHMIRYIV TILQEIGREN
1vs3A     174   --------qv a---egeagl evrlyfrgks flrgqvrgmv gtllevglgk
                                                                      
TARGET                  ss s          ssssssss       hhhhhh hhhhhhhh  
1vs3A                   ss s   ss  ss ssssssss       hhhhhh hhhhhhhh  


TARGET    183   EQPSLISQLL  --------- ---------- -------              
1vs3A     213   rppeslkail ktadrrlagp tapahglyfv eaaypee              
                                                                      
TARGET             hhhhhhh                                            
1vs3A              hhhhhhh hh              sssss sss

Quality 


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

 
Quaternary Structure Annotation of the Template 
 1vs3 is annotated as 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: 1vs3.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 (=DIMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.144 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 1vs3B

Template Selection 
 - Start SMR-Pipeline for:9c3a0196f5d44c6152f0bf12d570777f on BC2-cluster at Thu Feb 21 05:25:21
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
 - 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 1vs3A (82-273) 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:9c3a0196f5d44c6152f0bf12d570777f on BC2-cluster at Thu Feb 21 05:27:38
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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