SWISS-MODEL Repository - Model Details

Model Overview
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1
148

Sequence
UniProt O35427
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
O35427: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
RNA_pol_Rpb4

Model 3D Structure
Model information:
Modelled residue range: 1 to 122
Based on template: [ 2ckz ]  
Sequence Identity [%]: 33%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2ckz): HETERO DIMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ARG: 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       MEVKDANA ALLSNYEVFQ LLTDLKEQRK ESGKNKHSAG QQNL---NAI
2ckzC     1       mkvleern aflsdyevlk fltdlekkhl wdqkslaalr pynhpelqgi
                                                                      
TARGET                         hhhhhh hhhhhhhhh    hhhhh            hh
2ckzC                          hhhhhh hhhhhhhhh    hhhhhh          hhh


TARGET    46    TYETLKYISK TPCRNQSPAI VQEFLTAMKS HKLTKAEKLQ LLNHRPMTAV
2ckzC     59    trnvvnylsi i--skmsdes faelmtklns fklfkaeklq ivnqlpanmv
                                                                      
TARGET          hhhhhhhh          hhh hhhhhhhhh      hhhhhh hhh     hh
2ckzC           hhhhhhh           hhh hhhhhhhhh      hhhhhh hhh      h


TARGET    96    EIQLMVEESE ERLTEEQIEA LLHTVTS                         
2ckzC     133   hlysiveecd arfdektiee mleiisay                        
                                                                      
TARGET          hhh             hhhhh hhhhhh                          
2ckzC           hhh            hhhhhh hhhhhh

Quality 


Template's ligands section 
Ligands in the template: ARG: 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 
 2ckz 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: 2ckz.pdb2.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 2ckz_2

Template Selection 
 - Start SMR-Pipeline for:3a1af98959126f23dfd2d18ad5262a73 on BC2-cluster at Sat Feb 23 05:23:01
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
 - No template with D 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:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -  ******************************************************************
 - building model based on 2ckzC (1-122) 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:3a1af98959126f23dfd2d18ad5262a73 on BC2-cluster at Sat Feb 23 05:23:45
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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