SWISS-MODEL Repository - Model Details

Model Overview
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1
70

Sequence
UniProt Q9W5N2
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9W5N2: 7227.FBpp0110412

Domain
Link to: [ InterPro ]
Ribosomal_L38e

Model 3D Structure
Model information:
Modelled residue range: 1 to 69
Based on template: [ 3izr ]  
Sequence Identity [%]: 62%
Model date: 2013-02-22
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       MPREIKEV KDFLNKARRS DARAVKIKKN PTNTKFKIRC SRFLYTLVVQ
3izrn     1       mpkqihei kdflltarrk darsvrikrt kdavkfkvrc skylytlcvf
                                                                      
TARGET               hhhhh hhhhhhh       sssssss   sssssss            
3izrn                hhhhh hhhhhhh       sssssss   sssssss            


TARGET    49    DKEKADKIKQ SLPPGLQVKE V                               
3izrn     49    dadkanklkq slppgltvqe v-                              
                                                                      
TARGET           hhhhhh                                               
3izrn            hhhhhh

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:40ed3bf90010bc58fd718fe6ba193c21 on BC2-cluster at Fri Feb 22 04:45:01
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 (1-69) 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:40ed3bf90010bc58fd718fe6ba193c21 on BC2-cluster at Fri Feb 22 04:45:29
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 ]  

1-69 3izrn 62%
[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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