SWISS-MODEL Repository - Model Details

Model Overview
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1
71

Sequence
UniProt Q8K2X8
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q8K2X8: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
Tbf5

Model 3D Structure
Model information:
Modelled residue range: 1 to 71
Based on template: [ 2jnj ]  
Sequence Identity [%]: 98%
Model date: 2013-05-07
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (2jnj): 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 ]

Alignment 

TARGET    1          MVNVL KGVLIECDPA MKQFLLYLDE ANALGKKFII QDIDDTHVFV
2jnjB     1     gsh--mvnvl kgvliecdpa mkqfllylde snalgkkfii qdiddthvfv
                                                                      
TARGET                       sss    h hhhhhhhhhh h          sss   ssss
2jnjB                        sss    h hhhhhhhhhh h          sss   ssss


TARGET    46    IAELVNVLQE RVGELMDQNA FSLTQK                          
2jnjB     49    iaelvnvlqe rvgelmdqna fsltqk-                         
                                                                      
TARGET               hhhhh hh   hh                                    
2jnjB                hhhhh hh   hh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 2jnj is annotated as DIMER 
 The template structure (2jnj) was solved by NMR and does not contain any quaternary structure annotation 
 The template is annotated by the number of chains found in the PDB file 
      
 
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 0.48 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 2jnjA

Template Selection 
 - Start SMR-Pipeline for:b8ffb916ad73e3d71d7102844cffdb1e on BC2-cluster at Tue May  7 14:26:14
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

 - No A3m found

 - 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 2jnjB (1-71) 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:b8ffb916ad73e3d71d7102844cffdb1e on BC2-cluster at Tue May  7 14:27:07
2013


Template Description
Match Chain SeqId

2jnj: SOLUTION STRUCTURE OF THE P8 TFIIH SUBUNIT
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-71 2jnjA 99%
[Model]
1-71 2jnjB 99%
[Model]

1ydl: CRYSTAL STRUCTURE OF THE HUMAN TFIIH, NORTHEAST STRUCTURALGENOMICS TARGET HR2045.
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

6-71 1ydlA 97%
[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.