SWISS-MODEL Repository - Model Details

Model Overview
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1
189

Sequence
UniProt Q95Y90
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q95Y90: 6239.R13A5.8.1

Domain
Link to: [ InterPro ]
Ribosomal_L6
Ribosomal_L6

Model 3D Structure
Model information:
Modelled residue range: 10 to 182
Based on template: [ 2zkr ]  
Sequence Identity [%]: 64%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2zkre): 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       VVFPEGVT FTVKNRIVHV TGPRGTIRKD FRHLHMEMER IGKST--LRV
2zkre     10      vdipenvd itlkgrtviv kgprgtlrrd fnhinvelsl lgkkkkrlrv
                                                                      
TARGET                   s ssss sssss ss  ssssss s     sss          ss
2zkre                    s ssss sssss ss  ssssss s     ssss sss ssssss


TARGET    47    RKWFGVRKEL AAIRTVCSHI KNMIKGVTVG FRYKMRSVYA HFPINVTLQD
2zkre     58    dkwwgnrkel atvrticshv qnmikgvtlg frykmrsvya hfpinvviqe
                                                                      
TARGET          s     hhhh hhhhhhhhhh hhhhhhhhh  ssssssss       sssss 
2zkre           s     hhhh hhhhhhhhhh hhhhhhhhh  ssssssss       sssss 


TARGET    97    GNRTVEIRNF LGEKIVRRVP LPEGVIATIS TAQKDEIVVE GNDVQFVSQA
2zkre     108   ngslveirnf lgekyirrvr mrpgvacsvs qaqkdelile gndielvsns
                                                                      
TARGET            ssssss         ssss s    sss       ssssss s  hhhhhhh
2zkre             ssssss         ssss s    sssss ss sssssss s  hhhhhhh


TARGET    147   AARIQQSTAV KEKDIRKFLD GIYVSEK                         
2zkre     158   aaliqqattv knkdirkfld giyvsek-                        
                                                                      
TARGET          hhhhhhh               sssssss                         
2zkre           hhhhhhh               sssss

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:316aead895a1566a04326044b599bfcf on BC2-cluster at Wed Feb 20 23:28:45
2013 


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

FATAL - No A3m found

 - 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 2zkre (10-182) 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:316aead895a1566a04326044b599bfcf on BC2-cluster at Wed Feb 20 23:29:22
2013


Template Description
Match Chain SeqId

2zkr: STRUCTURE OF A MAMMALIAN RIBOSOMAL 60S SUBUNIT WITHIN AN 80S COMPLEX OBTAINED BY DOCKING HOMOLOGY MODELS OF THE RNAND PROTEINS INTO AN 8.7 A CRYO-EM MAP
Solved by: X-RAY, Resolution: 8.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

10-182 2zkre 64%
[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.