SWISS-MODEL Repository - Model Details

Model Overview
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1
597

Sequence
UniProt Q11181
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q11181: 6239.C05D10.4b

Domain
Link to: [ InterPro ]

Model 3D Structure
Model information:
Modelled residue range: 405 to 464
Based on template: [ 4nl9 ]  
Sequence Identity [%]: 18%
Model date: 2014-09-19
Revision date: 2014-09-17

Quaternary structure information: [details]
Template (4nl9): HETERO DIMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: MG: 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 2014-09-17. 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       DDVLLWLQ SAQMDDVAGL LIGYDLRGED LLQWNDQTLA QLGVSNPEIR
4nl9D     7       deltgilk klslekyqpi feeqevdmea fltltdgdlk elgiktdgsr
                                                                      
TARGET             hhhhhhh hh   hhhhh hhhh   hhh hh   hhhhh hh     hhh
4nl9D              hhhhhhh hh      hh hhhh   hhh hh   hhhhh hh    hhhh


TARGET    49    KKLLDDLSKI IE                                         
4nl9D     55    qqilaaisel nag                                        
                                                                      
TARGET          hhhhhhhhhh hh                                         
4nl9D           hhhhhhhhhh hh                                         



Quality


Template's ligands section
Ligands in the template: MG: 1.
Ligands in the template that will be assessed: MG101.
Model's ligands section
MG101
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand D.MG101 will not be included in the final model.
MG101: conservation:False, RMSD:False, included: False

No ligands were included in the model.


Quaternary Structure Annotation of the Template
4nl9 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: 4nl9.pdb2.gz

Quaternary Structure Modelling of the Target Protein
4nl9_2


Template Selection
 - Start SMR-Pipeline for:9cbe302d371d61b5bd50e49e6b5c7412 on BC2-cluster at Fri Sep 19 08:28:01
2014 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - 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 4nl9D (405-464) 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:9cbe302d371d61b5bd50e49e6b5c7412 on BC2-cluster at Fri Sep 19 08:28:43
2014 




Template Description
Match Chain SeqId

4nl9: CRYSTAL STRUCTURE OF THE HUMAN ANKS3-SAM/ANKS6-SAM HETEROD
Solved by: X-RAY, Resolution: 1.50A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

401-462 4nl9A 11%
[Model]
406-464 4nl9C 17%
[Model]
405-464 4nl9B 12%
[Model]
405-464 4nl9D 18%
[Model]

4nj8: CRYSTAL STRUCTURE OF THE HUMAN ANKS3 SAM DOMAIN L52A MUTAN
Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

399-462 4nj8A 11%
[Model]
405-466 4nj8B 11%
[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.




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