SWISS-MODEL Repository - Model Details

Model Overview
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1
257

Sequence
UniProt P48154
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P48154: 6239.F56F3.5

Domain
Link to: [ InterPro ]
Ribosomal_S3Ae

Model 3D Structure
Model information:
Modelled residue range: 20 to 232
Based on template: [ 3u5g ]  
Sequence Identity [%]: 56%
Model date: 2013-02-20
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3u5g): HETERO 34-mer
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        VDPFSRK EWYDIKAPNM FNTRQVGKTL INRTQGTKIA SEGLKGRVFE
3u5gB     20    v--vdpftrk ewfdikapst fenrnvgktl vnkstglksa sdalkgrvve
                                                                      
TARGET                  ss sssssss       sssssss sss              ssss
3u5gB                   ss sssssss       sssssss sss              ssss


TARGET    48    VSLGDLNNSE -ADFRKFKLI AEDVQGKNVL TNFHAMSMTH DKLCSIVKKW
3u5gB     68    vcladlqgse dhsfrkiklr vdevqgknll tnfhgmdftt dklrsmvrkw
                                                                      
TARGET          ssshhhh        ssssss sssss ssss sssssss    hhhhh     
3u5gB           ssshhhh        ssssss sssss ssss sssssss    hhhhh     


TARGET    97    HTLIEANTAV KTTDGYTLRV FVIAFTKKSV NQVKKTSYTK TSKIRKIRSE
3u5gB     118   qtlieanvtv ktsddyvlri faiaftrkqa nqvkrhsyaq sshirairkv
                                                                      
TARGET           sssssssss ss  ssssss ssssss                hhhhhhhhhh
3u5gB            sssssssss ss   sssss ssssss                hhhhhhhhhh


TARGET    147   MIGCIEKEVT GCDLKEVVSK LIPDSIGKDI EKTCSKLYPL QEVYIRKVKI
3u5gB     168   iseiltkevq gstlaqltsk lipevinkei enatkdifpl qnihvrkvkl
                                                                      
TARGET          hhhhhhhhh     hhhhhhh h   hhhhhh hhhhhhh       sssssss
3u5gB           hhhhhhhh      hhhhhhh h   hhhhhh hhhhhhh       sssssss


TARGET    197   IKRPKVDLGR LHDLHGD                                    
3u5gB     218   lkqpkfdvga lmalhgeg                                   
                                                                      
TARGET          ssss    hh hhhh                                       
3u5gB           s       hh hhhh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3u5g is annotated as HETERO 34-mer 
 The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry 
 The following biological unit was used to build the template structure: 3u5g.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3u5g_1

Template Selection 
 - Start SMR-Pipeline for:1e5352ba3b17d3f8b176ba8accc13405 on BC2-cluster at Wed Feb 20 10:19:38
2013 


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

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with A found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with P found
 - No template with Q found
 - No template with R found
 - No template with S found
 - No template with T found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with a found
 - No template with b found
 - No template with c found
 - No template with d found
 - No template with e found
 - No template with f found
 - No template with g found
 - No template with h 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 3u5gB (20-232) 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:1e5352ba3b17d3f8b176ba8accc13405 on BC2-cluster at Wed Feb 20 10:20:57
2013


Template Description
Match Chain SeqId

3j20: PROMISCUOUS BEHAVIOR OF PROTEINS IN ARCHAEAL RIBOSOMES REVCRYO-EM: IMPLICATIONS FOR EVOLUTION OF EUKARYOTIC RIBOSOMRIBOSOMAL SUBUNIT)
Solved by: X-RAY, Resolution: 6.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

19-223 3j20A 30%
[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.