SWISS-MODEL Repository - Model Details

Model Overview
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1
622

Sequence
UniProt Q3UY23
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q3UY23: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
FDX-ACB
DUF2431

Model 3D Structure
Model information:
Modelled residue range: 487 to 598
Based on template: [ 3cmq ]  
Sequence Identity [%]: 35%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3cmq): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: FA5: 1, MG: 1.
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 

                                                       
3cmqA     11    pgsvvellgk sypqddhsnl trkvltrvgr nlhnqqhhpl wlikervkeh
                                                                      
                                                       
3cmqA             sssss  s ssss        hhhhh             hh hhhhhhhhhh


                                                       
3cmqA     61    fykqyvgrfg tplfsvydnl spvvttwqnf dsllipadhp srkkgdnyyl
                                                                      
                                                       
3cmqA           hhhhhhh        sss     ssssshhh                    sss


                                                       
3cmqA     111   nrthmlraht sahqwdllha gldaflvvgd vyrrdqidsq hypifhqlea
                                                                      
                                                       
3cmqA             sssss    h   hhhhh    ssssssss sss          ssssssss


                                                       
3cmqA     161   vrlfskhelf agikdgeslq lfeqssrsah kqethtmeav klvefdlkqt
                                                                      
                                                       
3cmqA           ssss hhhh             sss           ssshhhh hhhhhhhhhh


                                                       
3cmqA     211   ltrlmahlfg deleirwvdc yfpfthpsfe meinfhgewl evlgcgvmeq
                                                                      
                                                       
3cmqA           hhhhhhhhh     sssssss    sssssss sssss  sss sssssssssh


TARGET    1                         I NLDLLVMLAY GISDWRILWT FDNRFLKRFA
3cmqA     261   qlvnsagaqd rigwafg--l glerlamily dipdirlfwc ederflkqfc
                                                                      
TARGET                                 hhhhhhhhh      hhh     hhhhhh  
3cmqA           hhhhh       ssssss  s sshhhhhhhh      hhh     hhhhhh  


TARGET    32    PGKIEH---F KSYSLYPPCY VHDVSFWVDE KKAFDELEFH TVARAVSQDT
3cmqA     309   vsninqkvkf qplskyp-av indisfwlps en-yaendfy dlvrtiggdl
                                                                      
TARGET                              s ssssssss         hhhh hhhhhhh  s
3cmqA                               s ssssssss         hhhh hhhhhhh  s


TARGET    79    VVSVQYRDRF QHPETRQVSL CYRLTYQTCD KALT ----- ----------
3cmqA     357   vekvdlidkf vhpkthktsh cyrityrhme rtlsqrevrh ihqalqeaav
                                                                      
TARGET          ssssssssss ss    ssss sssssss                         
3cmqA           ssssssssss ss    ssss sssssss        hhhhhh hhhhhhhhhh


TARGET          ---------                                             
3cmqA     407   qllgvegrf                                             
                                                                      
TARGET                                                                
3cmqA           hh   sss

Quality 


Template's ligands section 
Ligands in the template: FA5: 1, MG: 1. 
Ligands in the template that will be assessed: MG416. 
Model's ligands section 
MG416 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand A.MG416 will not be included in the final model. 
MG416: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 3cmq is annotated as MONOMER 
 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: 3cmq.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The target and template sequences are too diverse (seqid: 35.652) to infer a conservation of the oligomeric state 
 Please use the advancend features of the SwissModel Project Mode 
       
 The target structure was calculated as SINGLE CHAIN

Template Selection 
 - Start SMR-Pipeline for:c5be6f326f98bc47ae96405491caced1 on BC2-cluster at Sat Feb 23 04:11:27
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: 
 - Warning: Oligomer Prediction was not successfull!

 - 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 3cmqA (487-598) was successful 
 -                                             *******
 - building model based on 4ex5B (343-398) 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:c5be6f326f98bc47ae96405491caced1 on BC2-cluster at Sat Feb 23 04:12:38
2013


Template Description
Match Chain SeqId

4ex5: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE LYSRS FROM BURKTHAILANDENSIS BOUND TO LYSINE
Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

343-398 4ex5A 18%
[Model]
343-398 4ex5B 18%
[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.