SWISS-MODEL Repository - Model Details

Model Overview
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1
584

Sequence
UniProt P13645
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P13645: 9606.ENSP0000026

Domain
Link to: [ InterPro ]
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Model 3D Structure
Model information:
Modelled residue range: 366 to 455
Based on template: [ 3tnu ]  
Sequence Identity [%]: 66%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3tnu): HETERO TETRAMER
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       TELRRNVQ ALEIELQSQL ALKQSLEASL AETEGRYCVQ LSQIQAQISA
3tnuA     332     selrrtmq nleielqsql smkaslensl eetkgrycmq laqiqemigs
                                                                      
TARGET             hhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh
3tnuA              hhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh


TARGET    49    LEEQLQQIRA ETECQNTEYQ QLLDIKIRLE NEIQTYRSLL EG        
3tnuA     380   veeqlaqlrc emeqqnqeyk illdvktrle qeiatyrrll eg-       
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhh   hh h         
3tnuA           hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhh   hh h

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3tnu is annotated as HETERO TETRAMER 
 PISA was used to annotate the quaternary structure, because the author assignment was ambigous (i.e the same chains appear in different biolgoical units annotated by the author) 
  A biological unit file could be identified with the same complex description as the PISA annotation and was used to build the assembly: 3tnu.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3tnu_1

Template Selection 
 - Start SMR-Pipeline for:d339d642a40972befdcbbc146ad7f302 on BC2-cluster at Sat Feb 23 08:33:20
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

FATAL - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with B 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:4): model based on new templates
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                   ************
 - building model based on 3tnuA (366-455) was successful 
 -                             ***********
 - building model based on 3swkA (205-287) was successful 
 -                                            *********
 - building model based on 3kltB (313-381) was successful 
 -                     *************
 - building model based on 3s4rA (145-237) 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:d339d642a40972befdcbbc146ad7f302 on BC2-cluster at Sat Feb 23 08:34:45
2013


Template Description
Match Chain SeqId

3tnu: HETEROCOMPLEX OF COIL 2B DOMAINS OF HUMAN INTERMEDIATE FILPROTEINS, KERATIN 5 (KRT5) AND KERATIN 14 (KRT14)
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

366-455 3tnuA 67%
[Model]

4gkw: CRYSTAL STRUCTURE OF THE COILED-COIL DOMAIN OF C. ELEGANS
Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

203-225 4gkwA 17%
[Model]
203-225 4gkwB 17%
[Model]

4hpq: CRYSTAL STRUCTURE OF THE ATG17-ATG31-ATG29 COMPLEX
Solved by: X-RAY, Resolution: 3.06A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

152-159 4hpqC 38%
[Model]
152-159 4hpqF 38%
[Model]
416-427 4hpqC 8%
[Model]
416-427 4hpqF 8%
[Model]
425-447 4hpqC 17%
[Model]
425-447 4hpqF 17%
[Model]

4ad8: CRYSTAL STRUCTURE OF A DELETION MUTANT OF DEINOCOCCUS RADIRECN
Solved by: X-RAY, Resolution: 4.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

442-456 4ad8A 13%
[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.