SWISS-MODEL Repository - Model Details

Model Overview
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1
760

Sequence
UniProt Q9JK91
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
DNA_mis_repair
HATPase_c_3

Model 3D Structure
Model information:
Modelled residue range: 492 to 755
Based on template: [ 3rbn ]  
Sequence Identity [%]: 89%
Model date: 2013-02-17
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3rbn): 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                KEMTAACYPR RRIINLTSVL SLQEEISERC HETLREMLRN
3rbnA     10    grenlyfr-- kextaactpr rriinltsvl slqeeineqg hevlrexlhn
                                                                      
TARGET                      sss   sss       hhhh hhhhhhh    hhhhhhhhh 
3rbnA                       sss   sss       hhhh hhhhhhh    hhhhhhhhh 


TARGET    41    HSFVGCVNPQ WALAQHQTKL YLLNTTKLSE ELFYQILIYD FANFGVLRLS
3rbnA     61    hsfvgcvnpq walaqhqtkl yllnttklse elfyqiliyd fanfgvlrls
                                                                      
TARGET           ssssss  s ssssss sss ssssshhhhh hhhhhhhhhh     sssss 
3rbnA            ssssss  s ssssss sss ssssshhhhh hhhhhhhhhh     sssss 


TARGET    91    EPAPLFDLAM LALDSPESGW TEDDGPKEGL AEYIVEFLKK KAEMLADYFS
3rbnA     111   epaplfdlax laldspesgw teedgpkegl aeyiveflkk kaexladyfs
                                                                      
TARGET            ssshhhhh hhh              hhhh hhhhhhhhh    hhhhhh s
3rbnA             ssshhhhh hhh              hhhh hhhhhhhhh    hhhhhh s


TARGET    141   VEIDEEGNLI GLPLLIDSYV PPLEGLPIFI LRLATEVNWD EEKECFESLS
3rbnA     161   leideegnli glpllidnyv ppleglpifi lrlatevnwd eekecfesls
                                                                      
TARGET          ssss  ssss ssss             hhhh hhhhh       hhhhhhhhh
3rbnA           ssss  ssss ssss             hhhh hhhhh       hhhhhhhhh


TARGET    191   KECAMFYSIR KQYILEESTL SGQQSDMPGS TSKPWKWTVE HIIYKAFRSH
3rbnA     211   kecaxfysir kqyiseestl sns------- ----wkwtve hivykalrsh
                                                                      
TARGET          hhhhhhh               sssss    s ssss hhhhh hhhhhhh   
3rbnA           hhhhhhh         sss    ss            shhhh    hhhhh   


TARGET    241   LLPPKHFTED GNVLQLANLP DLYK                            
3rbnA     261   ilppkhfted gnilqlanlp dlyk-                           
                                                                      
TARGET               hh     ssssssss                                  
3rbnA                hh     ssssssss

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3rbn is annotated as DIMER 
 PISA was used to annotate the quaternary structure, because the author assignment was not complete  
  A biological unit file could be identified with the same complex description as the PISA annotation and was used to build the assembly: 3rbn.pdb1.gz 
      
 
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 0.228 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 3rbnB

Template Selection 
 - Start SMR-Pipeline for:35e5c8bdedf91410a25307cf7b8c84e4 on BC2-cluster at Sun Feb 17 08:30:09
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  2
 - 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
 - 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 3rbnA (492-755) was successful 
 - ***********************************
 - building model based on 3na3A (3-335) 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:35e5c8bdedf91410a25307cf7b8c84e4 on BC2-cluster at Sun Feb 17 08:34:55
2013


Template Description
Match Chain SeqId

3rbn: CRYSTAL STRUCTURE OF MUTL PROTEIN HOMOLOG 1 ISOFORM 1 [HOM
Solved by: X-RAY, Resolution: 2.16A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

496-755 3rbnB 86%
[Model]
492-755 3rbnA 90%
[Model]

3na3: MUTL PROTEIN HOMOLOG 1 ISOFORM 1 FROM HOMO SAPIENS
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-335 3na3A 86%
[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.