SWISS-MODEL Repository - Model Details

Model Overview
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1
796

Sequence
UniProt Q10003
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q10003: 6239.T05H10.7a

Domain
Link to: [ InterPro ]
CBM_20
GDPD

Model 3D Structure
Model information:
Modelled residue range: 405 to 702
Based on template: [ 3ch0 ]  
Sequence Identity [%]: 24%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3ch0): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: EDO: 1, GOL: 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 

TARGET    1                    GHRGAG NSYTKFAMAR ENTIHSLNTA AKNGADYVEF
3ch0A     0     gxiqvpasfd iq--ghrgcr ------gllp entiaaftka lllgvttlef
                                                                      
TARGET                         sss  s ss   sss      hhhhhhh hhh  sssss
3ch0A                    s ss  sss                  hhhhhhh hhh  sssss


TARGET    37    DVQLTKDRIA VIYHD--FHV LVSVARRDGL AMPPPMTREQ LDSSNLDYHE
3ch0A     42    dlviskdnrv vvshdtffhh eitx------ -xvdgedvte aneknfnlya
                                                                      
TARGET          sssss   ss sss             hhhh                       
3ch0A           sssss   ss sss  sss                              sss  


TARGET    85    LPVKDLKLSQ LKLLMLDHLS FPQKKEN--V KKLVEAGEEE EDFKPFPTLL
3ch0A     86    xnyadik--e idvgxkthpr fksqkkvpav kpl------- -----freli
                                                                      
TARGET            hhhhh                                          hhhhh
3ch0A             hhhhh                           ss             shhhh


TARGET    133   EALTKVDPDV GFNVEVKYPM MQNNGEHECD HYFERNLFVD VILADVMKHA
3ch0A     121   etaeklsaki qyngeikstv egdnidhp-- ---nialfcd lvvaeikkah
                                                                      
TARGET          hhhhhh     ssssss                    hhhhhh hhhhhhhhh 
3ch0A           hhhhhh     sssssss                   hhhhhh hhhhhhhhh 


TARGET    183   GNRRIMFSSF DPDICSMVAT KQNKYPVLFL CVGETQRYTP FQDQRTSTSM
3ch0A     166   itdrftlqsf d---vraley xhsqypdikl sylvetkgt- lkkqleklsf
                                                                      
TARGET             ssssss       hhhhh hhhh    ss ssss        hhhhh    
3ch0A              ssssss      hhhhhh hhhh    ss ssss       hhhhhh    


TARGET    233   TAVNFAAGAD LLGVNFNSED LLKDPMPVKK ANEFGMVTFV WGEDLDKKEN
3ch0A     212   tpavyspdvt lvsk------ --kd---ida ahklgxrvip w--tvntkee
                                                                      
TARGET            ssssss       sss    sss     hh hhhh  sss         hhh
3ch0A             ssssss      h         hh   hhh hhhh  ssss s      hhh


TARGET    283   INYFKKELGV DGVIYD --- ----                            
3ch0A     249   ietl-islgv dgiitdypdl ffek                            
                                                                      
TARGET          hhhh                                                  
3ch0A           hhhh hhh   sssss   hh

Quality 


Template's ligands section 
Ligands in the template: EDO: 1, GOL: 1. 
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 3ch0 is annotated as MONOMER 
 PISA was used to annotate the quaternary structure, because the author assignment was not complete  
 PISA annotates this structure as Monomer, therefore the corresponding PDB chain was used as template structure 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.34 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:f4a31c9413191065a1d204a01b5bda42 on BC2-cluster at Thu Feb 21 15:31:55
2013 


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

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - 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 3ch0A (405-702) 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:f4a31c9413191065a1d204a01b5bda42 on BC2-cluster at Thu Feb 21 15:34:41
2013

no data available!
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.