SWISS-MODEL Repository - Model Details

Model Overview
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1
1465

Sequence
UniProt P33609
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P33609: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
DNA_pol_B
DNA_pol_B_exo1
zf-DNA_Pol
DNA_pol_alpha_N

Model 3D Structure
Model information:
Modelled residue range: 1351 to 1381
Based on template: [ 1k0p ]  
Sequence Identity [%]: 77%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1k0p): MONOMER
Model: MONOMER

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       ICEEPTCC SRLRRLPLHF SRNGPLCPVC MKA                  
1k0p_1#1  1       iceeptcr nrtrhlplqf srtgplcpac mka-                 
                                                                      
TARGET                  hh hhh                                        
1k0p_1#1                hh hhhhhh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 1k0p is annotated as MONOMER 
 The template structure (1k0p) 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 
 The quaternary structure can be assumed to be identical 
 Model was succesfully built as MONOMER.

Template Selection 
 - Start SMR-Pipeline for:06ba28e798a66970e13c52b5e2d9b5c9 on BC2-cluster at Sat Feb 23 02:17:35
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 B found
 - No template with A found
 - No template with G found
 - No template with C found
 - No template with E found
 - 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 1k0pA (1351-1381) was successful 
 -                                               ***********
 - building model based on 1s5jA (841-1049) was not successful go to next best template
 -                                               *********
 - building model based on 2p5gB (843-1015) was not successful go to next best template
 -                                               *********
 - building model based on 2p5oC (843-1015) was successful 
 -                                  **********************************
 - Oligomeric modeling of 1tgoA was not successful, fall back to monomeric modeling
 - building model based on 1tgoA (605-1227) was not successful go to next best template
 -                                  **********************************
 - building model based on 2vwkA (605-1227) was successful 
 -                                                                       ********
 - building model based on 3floB (1273-1426) 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:06ba28e798a66970e13c52b5e2d9b5c9 on BC2-cluster at Sat Feb 23 02:25:53
2013


Template Description
Match Chain SeqId

1k0p: NMR STRUCTURES OF THE ZINC FINGER DOMAIN OF HUMAN DNA POLYMERASE-ALPHA
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1351-1381 1k0pA 77%
[Model]

1k18: MINIMIZED AVERAGE NMR STRUCTURE OF THE ZINC FINGER DOMAIN OF HUMAN DNA POLYMERASE-ALPHA
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1351-1381 1k18A 77%
[Model]

1n5g: NMR STRUCTURES OF THE ZINC FINGER DOMAIN OF HUMAN DNA POLYMERASE-ALPHA
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1349-1386 1n5gA 76%
[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.