SWISS-MODEL Repository - Model Details

Model Overview
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1
309

Sequence
UniProt P53881
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P53881: 4932.YNL177C

Domain
Link to: [ InterPro ]
Ribosomal_L22

Model 3D Structure
Model information:
Modelled residue range: 160 to 271
Based on template: [ 3zf7 ]  
Sequence Identity [%]: 13%
Model date: 2013-04-29
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (3zf7R): 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 ]

Alignment 

TARGET    1                  EPSVYAQS YRIKSSMKKA TLLLRLLGGL DVMKAISQCH
3zf7R     2     vhysrkpqvs --sktakaki adlrchyknt fetanvingm klrkaqqlyr
                                                                      
TARGET                          sssss ss    hhhh hhhhhhh       hhhhhhh
3zf7R                           sssss ss    hhhh hhhhhhh       hhhhhhh


TARGET    39    FS-------- ---------- ---------- ----NKKIAR EVAELLQKGV
3zf7R     50    qvlaktrcip fkryngkign taqakewgqt kgrwprksvv amlsllknae
                                                                      
TARGET                                                    h hhhhhhhhhh
3zf7R           hhh     ss s                     sss   hhhh hhhhhhhhhh


TARGET    57    KDGQKLGLKP EDLYISQIWT GSDGFWRKRV EFKARTRIGI ISHPYIHVRC
3zf7R     100   anaiekgldp gkmvikhvqv d-qaprvrrr tfrahgritp ymrspchvql
                                                                      
TARGET          hhhhhh        sssssss s     ssss sss   ssss sss  sssss
3zf7R           hhhhhh        sssssss s     ssss sss   ssss sss  sssss


TARGET    107   ILRTKS                                                
3zf7R     149   fmtqpqe                                               
                                                                      
TARGET          sss                                                   
3zf7R           sss

Quality 


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

 
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:b6612ae221041f76701c26bc806f275c on BC2-cluster at Mon Apr 29 04:11:27
2013 


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

 - No A3m found

 - 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!

 - Warning: clustersMergedFile not found
 - 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 3zf7R (160-271) 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:b6612ae221041f76701c26bc806f275c on BC2-cluster at Mon Apr 29 04:12:10
2013


Template Description
Match Chain SeqId

3zf7: HIGH-RESOLUTION CRYO-ELECTRON MICROSCOPY STRUCTURE OF THE BRUCEI RIBOSOME
Solved by: X-RAY, Resolution: 5.57A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

160-271 3zf7R 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.