SWISS-MODEL Repository - Model Details

Model Overview
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1
445

Sequence
UniProt O17919
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
O17919: 6239.K01G5.5.1

Domain
Link to: [ InterPro ]
PUA
TruB_N
DKCLD

Model 3D Structure
Model information:
Modelled residue range: 38 to 78
Based on template: [ 3zv0 ]  
Sequence Identity [%]: 68%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3zv0): HETERO TETRAMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: GOL: 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        SQWPLLL KNYDKLNVRT NHYTPHVEGV SPLKRDIKNY ISSG -----
3zv0D     19    t--sewplll knfdkllvrs ghytp----- iplkrdlksy issgpletll
                                                                      
TARGET                                                 hhhh           
3zv0D                                                  hhhh       hh  


TARGET          ---------- ---------- ---------- ---------- ----------
3zv0D     264   vgykrivvkd savnavcyga klmipgllry eegielydei vlittkgeai
                                                                      
TARGET                                                                
3zv0D              ssssss     hhhh     sss sssss s      sss ssss   sss


TARGET          ---------- ---------- ---------- ---------- ----------
3zv0D     314   avaiaqmstv dlascdhgvv asvkrcimer dlyprrwglg pvaqkkkqmk
                                                                      
TARGET                                                                
3zv0D           ssssss  hh hhhh   sss sssssss                hhhhhhhhh


TARGET          ---------- ----                                       
3zv0D     364   adgkldkygr vnen                                       
                                                                      
TARGET                                                                
3zv0D           hh

Quality 


Template's ligands section 
Ligands in the template: GOL: 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 
 3zv0 is annotated as HETERO TETRAMER 
 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: 3zv0.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3zv0_1

Template Selection 
 - Start SMR-Pipeline for:59bc8831099b5fcf4d6abf21a1e235c1 on BC2-cluster at Thu Feb 21 01:21:48
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  2 go for
modeling ...

 - No template with B found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -        *******
 - building model based on 3zv0D (38-78) was successful 
 -       *****************************************************************
 - building model based on 3uaiA (36-396) 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:59bc8831099b5fcf4d6abf21a1e235c1 on BC2-cluster at Thu Feb 21 01:22:59
2013


Template Description
Match Chain SeqId

3uai: STRUCTURE OF THE SHQ1-CBF5-NOP10-GAR1 COMPLEX FROM SACCHARCEREVISIAE
Solved by: X-RAY, Resolution: 3.06A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

36-396 3uaiA 67%
[Model]

3u28: CRYSTAL STRUCTURE OF A CBF5-NOP10-GAR1 COMPLEX FROM SACCHACEREVISIAE
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

36-368 3u28A 67%
[Model]

3zv0: STRUCTURE OF THE SHQ1P-CBF5P COMPLEX
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

276-394 3zv0D 66%
[Model]
276-394 3zv0C 66%
[Model]
38-78 3zv0C 61%
[Model]
38-78 3zv0D 68%
[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.