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Model Overview
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1
272

Sequence
UniProt P51403
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P51403: 6239.C49H3.11.1

Domain
Link to: [ InterPro ]
Ribosomal_S5
Ribosomal_S5_C

Model 3D Structure
Model information:
Modelled residue range: 97 to 245
Based on template: [ 2zkq ]  
Sequence Identity [%]: 83%
Model date: 2013-02-20
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2zkqe): 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       NLKDEVLK ISPVQKQTTA GQRTRFKAFV AIGDHAGHVG LGVKCSKEVA
2zkqe     9       slkdevlk ivpvqkqtra gqrtrfkafv aigdhnghvg lgvkcskeva
                                                                      
TARGET              ssssss ssssssss   ssssssssss ssss  ssss ssssss  hh
2zkqe               ssssss ssssssss   ssssssssss ssss  ssss ssssss  hh


TARGET    49    TAIRGAIVAA KLAVVPVRRG YWGNKIGLPH TVPCKVTGKC ASVMVRLIPA
2zkqe     57    tairgaiila klsivpvr-g ywgnkigkph tvpckvtgrs gsvpvrlipa
                                                                      
TARGET          hhhhhhhhhh hh  sss                    sssss  sssssss  
2zkqe           hhhhhhhhhh hh  sss                    sssss  sssssss  


TARGET    99    PRGTGIVSAP VPKKLLHMAG IEDCYTAAKG STATLGNFAK ATYAALQRTY
2zkqe     107   prgtgivsap vpkkllmmag iddcytsarg ctatlgnfak atfdaiskty
                                                                      
TARGET              sss     hhhhhhhh     sssssss s   hhhhhh hhhhhhhh  
2zkqe               sss     hhhhhhhh     sssssss s   hhhhhh hhhhhhhh  


TARGET    149   S                                                     
2zkqe     157   s-                                                    
                                                                      
TARGET                                                                
2zkqe

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:ec127a416c7ac7c05408ccfae6ccb7f0 on BC2-cluster at Wed Feb 20 11:10:53
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  2
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
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 - No template with T found
 - No template with C found
 - No template with G found
 - No template with H found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with C found
 - No template with G found
 - No template with I found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with K found
 - No template with M found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with S found
 - No template with R found
 - No template with T found
 - No template with W found
 - No template with V found
 - No template with A found
 - No template with R found
 - No template with V found
 - No template with A found
 - No template with R found
 - No template with V found
 - No template with D found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with C found
 - No template with B found
 - No template with D found
 - No template with G found
 - No template with F found
 - No template with I found
 - No template with H found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with S found
 - No template with R found
 - No template with U found
 - No template with W found
 - No template with C found
 - No template with D found
 - No template with I found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with H found
 - No template with K found
 - No template with C found
 - No template with G found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with U found
 - No template with J found
 - No template with D found
 - No template with H found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with Q found
 - No template with D found
 - No template with G found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with P found
 - No template with T found
 - No template with G found
 - No template with C found
 - No template with P found
 - No template with H found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with N found
 - No template with Q found
 - No template with T found
 - No template with C found
 - No template with G found
 - No template with H found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with C found
 - No template with G found
 - No template with H found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with C found
 - No template with K found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with U found
 - No template with T found
 - No template with H found
 - No template with D found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with O found
 - No template with L found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with N found
 - No template with D found
 - No template with G found
 - No template with P found
 - No template with I found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with T found
 - No template with C found
 - No template with P found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with T found
 - No template with G found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with Q found
 - No template with P found
 - No template with S found
 - No template with R found
 - No template with T found
 - No template with W found
 - No template with D found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with G found
 - No template with K found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with S found
 - No template with T found
 - No template with W found
 - No template with G found
 - No template with H found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with e found
 - No template with d found
 - No template with i found
 - No template with h found
 - No template with j found
 - No template with m found
 - No template with l found
 - No template with o found
 - No template with n found
 - No template with q found
 - No template with p found
 - No template with r found
 - No template with u found
 - No template with v found
 - No template with C found
 - No template with G found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with D found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with G found
 - No template with I found
 - No template with H found
 - No template with K found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with F found
 - No template with K found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with S found
 - No template with R found
 - No template with T found
 - No template with W found
 - No template with X found
 - No template with K found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with S found
 - No template with R found
 - No template with T found
 - No template with W found
 - No template with D found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with D found
 - No template with G found
 - No template with P found
 - No template with K found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with I found
 - No template with T found
 - No template with C found
 - No template with B found
 - No template with G found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with Q found
 - No template with P found
 - No template with R found
 - No template with U found
 - No template with I found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with C found
 - No template with D found
 - No template with G found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with S found
 - No template with R found
 - No template with T found
 - No template with W found
 - No template with D found
 - No template with I found
 - No template with H found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with i found
 - No template with k found
 - No template with j found
 - No template with l found
 - No template with o found
 - No template with n found
 - No template with q found
 - No template with p found
 - No template with r found
 - No template with u found
 - No template with D found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with D found
 - No template with G found
 - No template with I found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with N found
 - No template with T found
 - No template with D found
 - No template with H found
 - No template with K found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with C found
 - No template with G found
 - No template with H found
 - No template with J found
 - No template with M found
 - No template with K found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with D found
 - No template with I found
 - No template with K found
 - No template with M found
 - No template with O found
 - No template with L found
 - No template with Q found
 - No template with P found
 - No template with T found
 - No template with N found
 - No template with D found
 - No template with P found
 - No template with K found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with I found
 - No template with T found
 - No template with Q found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with L found
 - No template with O found
 - No template with N found
 - No template with P found
 - No template with U found
 - No template with T found
 - No template with C found
 - No template with G found
 - No template with K found
 - No template with J found
 - No template with M found
 - No template with O found
 - No template with N found
 - No template with Q found
 - No template with P found
 - No template with U found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                              ********************************************
 - building model based on 2zkqe (97-245) was successful 
 -                *****************************************************************
 - building model based on 3iz6E (52-271) 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:ec127a416c7ac7c05408ccfae6ccb7f0 on BC2-cluster at Wed Feb 20 11:13:30
2013


Template Description
Match Chain SeqId

2zkq: STRUCTURE OF A MAMMALIAN RIBOSOMAL 40S 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 ]  

97-245 2zkqe 84%
[Model]

3iz6: LOCALIZATION OF THE SMALL 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 ]  

52-271 3iz6E 68%
[Model]

3u5g: THE STRUCTURE OF THE EUKARYOTIC RIBOSOME AT 3.0 A RESOLUTI
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

57-261 3u5gC 63%
[Model]

3u5c: THE STRUCTURE OF THE EUKARYOTIC RIBOSOME AT 3.0 A RESOLUTI
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

57-261 3u5cC 63%
[Model]

3jyv: STRUCTURE OF THE 40S RRNA AND PROTEINS AND P/E TRNA FOR EUKARYOTIC RIBOSOME BASED ON CRYO-EM MAP OF THERMOMYCES LANUGINOSUS RIBOSOME AT 8.9A RESOLUTION
Solved by: X-RAY, Resolution: 8.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

98-257 3jyvE 62%
[Model]

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 ]  

48-251 3j20F 43%
[Model]

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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.