SWISS-MODEL Repository - Model Details

Model Overview
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1
385

Sequence
UniProt Q9FNY2
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9FNY2: 3702.AT5G03415.1

Domain
Link to: [ InterPro ]
E2F_TDP
DP

Model 3D Structure
Model information:
Modelled residue range: 101 to 184
Based on template: [ 1cf7 ]  
Sequence Identity [%]: 71%
Model date: 2013-02-19
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1cf7): HETERO DIMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: DC: 1, DG: 2, DT: 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       GRGLRQFS MKVCEKVESK GRTTYNEVAD ELVAEFALPN NDGTSPDQQQ
1cf7B     68      gkglrhfs mkvcekvqrk gttsynevad elvseftnsn nhlaa--dsa
                                                                      
TARGET               hhhhh hhhhhhhhhh sss hhhhhh hhhhhhh              
1cf7B                hhhhh hhhhhhhhhh sss hhhhhh hhhhhhh              


TARGET    49    YDEKNIRRRV YDALNVLMAM DIISKDKKEI QWRGLP               
1cf7B     114   ydqknirrrv ydalnvlmam niiskekkei kwiglp-              
                                                                      
TARGET            hhhhhhhh hhhhhhhhh   sssss  ss sss                  
1cf7B             hhhhhhhh hhhhhhhhh   sssss  ss sss

Quality 


Template's ligands section 
Ligands in the template: DC: 1, DG: 2, DT: 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 
 1cf7 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: 1cf7.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 1cf7_1

Template Selection 
 - Start SMR-Pipeline for:8c469f02c8d9faff515fbbd36b8ab9f4 on BC2-cluster at Tue Feb 19 14:54:38
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with A found
 - No template with A found
 - No template with B found
 - No template with C 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 1cf7B (101-184) was successful 
 -                                        *********************
 - building model based on 2azeA (190-290) 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:8c469f02c8d9faff515fbbd36b8ab9f4 on BC2-cluster at Tue Feb 19 14:55:30
2013


Template Description
Match Chain SeqId

1cf7: STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP
Solved by: X-RAY, Resolution: 2.60A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

101-184 1cf7B 71%
[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.