SWISS-MODEL Repository - Model Details

Model Overview
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1
1078

Sequence
UniProt Q9V460
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9V460: 7227.FBpp0085716

Domain
Link to: [ InterPro ]
KOW
KOW
KOW
Spt5-NGN
Spt5_N
CTD

Model 3D Structure
Model information:
Modelled residue range: 213 to 306
Based on template: [ 3h7h ]  
Sequence Identity [%]: 75%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3h7h): HETERO 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 

TARGET    1        DPNLWMV KCRIGEEKAT ALLLMRKYLT YLNTDDPLQI KSIIAPEGVK
3h7hB     175   m--dpnlwtv kckigeerat aislmrkfia yqftdtplqi ksvvapehvk
                                                                      
TARGET               sssss ss    hhhh hhhhhhhhhh h           sss      
3h7hB                sssss ss    hhhh hhhhhhhhhh h           sss      


TARGET    48    GYIYLEAYKQ THVKTCIDNV GNLRMGKWKQ EMVPIKEMTD VLKVVKE   
3h7hB     223   gyiyveaykq thvkqaiegv gnlrlgywnq qmvpikemtd vlkvvke-  
                                                                      
TARGET          sssssss    hhhhhhh               sss     hh hh        
3h7hB           sssssss    hhhhhhh               sss     hh hh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3h7h 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: 3h7h.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3h7h_1

Template Selection 
 - Start SMR-Pipeline for:6fe891ab92c5983b588e358fa8efb4da on BC2-cluster at Fri Feb 22 01:48:20
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  4
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

FATAL - No A3m found

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

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:4): model based on new templates
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                 *******
 - building model based on 3h7hB (213-306) was successful 
 -                                      *****
 - building model based on 2do3A (504-564) was successful 
 -                                                        ****
 - building model based on 2e70A (738-790) was successful 
 -                                   ****
 - building model based on 2e6zA (461-512) 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:6fe891ab92c5983b588e358fa8efb4da on BC2-cluster at Fri Feb 22 01:49:48
2013


Template Description
Match Chain SeqId

3h7h: CRYSTAL STRUCTURE OF THE HUMAN TRANSCRIPTION ELONGATION FACTOR DSIF, HSPT4/HSPT5 (176-273)
Solved by: X-RAY, Resolution: 1.55A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

213-306 3h7hB 76%
[Model]

2do3: SOLUTION STRUCTURE OF THE THIRD KOW MOTIF OF TRANSCRIPTIONELONGATION FACTOR SPT5
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

504-564 2do3A 72%
[Model]

2e70: SOLUTION STRUCTURE OF THE FIFTH KOW MOTIF OF HUMAN TRANSCRIPTION ELONGATION FACTOR SPT5
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

738-790 2e70A 68%
[Model]

2e6z: SOLUTION STRUCTURE OF THE SECOND KOW MOTIF OF HUMAN TRANSCRIPTION ELONGATION FACTOR SPT5
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

461-512 2e6zA 67%
[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.