SWISS-MODEL Repository - Model Details

Model Overview
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1
134

Sequence
UniProt Q9SIM4
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9SIM4: 3702.AT2G20450.1

Domain
Link to: [ InterPro ]
Ribosomal_L14e

Model 3D Structure
Model information:
Modelled residue range: 1 to 134
Based on template: [ 3izr ]  
Sequence Identity [%]: 82%
Model date: 2013-02-18
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3izrN): Unknown
Model: 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       MGFKRFVE IGRVALVNYG EDYGKLVVIV DVVDQNRALV DAPDMERIQM
3izrN     1       mpfkrfve igrvalvnyg kdygrlvviv dvvdqnralv dapdmvrcqi
                                                                      
TARGET                        sss            sss        sss s      sss
3izrN                         sss            sss        sss s      sss


TARGET    49    NLKRLSLTDI VIDINRVPKK KVLIEAMEKA DVKNKWEKSS WGRKLIVQKR
3izrN     49    nfkrlsltdi kidikrvpkk ttlikameea dvknkwenss wgkklivqkr
                                                                      
TARGET               sss              hhhhhhhhh    hhhhhhh      hhhhhh
3izrN                sss              hhhhhhhhh    hhhhhhh      hhhhhh


TARGET    99    RAALNDFDRF KIMLAKIKRA GIVRQELAKL KREIAA               
3izrN     99    raslndfdrf kvmlakikrg gairqelakl kktaaa-              
                                                                      
TARGET          h      hhh hhhhhhh    hhhhhhhhhh hhhh                 
3izrN           hh     hhh hhhhhhhhhh hhhhhhhhhh hhhh

Quality 


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

 
Oligomer Annotation of the Template structure 
 Sorry, we haven't found any oligomeric annotation for this template. 
 Either the complex was too large (>60 chains) or the structures was excluded for other reasons. 
 Please contact help@swissmodel.org for more information!

Template Selection 
 - Start SMR-Pipeline for:250ea0e9aa76949f66c8da95349935ce on BC2-cluster at Mon Feb 18 22:16:11
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

 - 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 3izrN (1-134) 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:250ea0e9aa76949f66c8da95349935ce on BC2-cluster at Mon Feb 18 22:16:42
2013


Template Description
Match Chain SeqId

3izr: LOCALIZATION OF THE LARGE SUBUNIT RIBOSOMAL PROTEINS INTO CRYO-EM MAP OF TRITICUM AESTIVUM TRANSLATING 80S RIBOSOME
Solved by: X-RAY, Resolution: 5.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-134 3izrN 83%
[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.