SWISS-MODEL Repository - Model Details

Model Overview
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1
557

Sequence
UniProt Q99JT1
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q99JT1: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
GatB_Yqey
GatB_N

Model 3D Structure
Model information:
Modelled residue range: 62 to 492
Based on template: [ 3h0l ]  
Sequence Identity [%]: 42%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3h0l): HETERO TRIMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ADP: 1, MG: 1, ZN: 1.
Ligands in the model: MG: 1
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        KWAAVVG LEIHAQISSN SKLFSGAQVC FAAPPNSLVS YFDASLPGTL
3h0lH     3     e--kyeavig leihvqmdtk tkmfcgckve fgaepntnvc pvclgmpgal
                                                                      
TARGET               sssss sssssss  s ss    sss             h         
3h0lH              sssssss sssssss  s ss    sss             hhh       


TARGET    48    PVLNRRCVEA AVMTGLALNC HINKKSLFDR KHYFYSDLPA GYQITQQRLP
3h0lH     51    pivnkravey airaslalnc evheesvfar khyfypdlpk gyqisqyekp
                                                                      
TARGET              hhhhhh hhhhhhhh   ssssss sss sss        sssss     
3h0lH               hhhhhh hhhhhhhh   ssssss sss sss        sssss     


TARGET    98    IAANGHLTYC IYLGKKPSQV TTKTVRIKQI QLEQDSGKSL HDDLRSQTLI
3h0lH     101   latngwveln lpngek---- --kkvrirrl hieedagkni heg--dktlv
                                                                      
TARGET          sss sssss               ssssssss sssss  sss ss    ssss
3h0lH           sss ssssss s   ss       ssssssss sssss  sss ss    ssss


TARGET    148   DLNRAGIGLL EVVLEPDLCC GEEAALAVRE LQLILQALGT SQANMAEGQL
3h0lH     143   dlnragtplm eivtepdirt peearlflek lrnimryagv skadmekgql
                                                                      
TARGET          s     ssss sssss      hhhhhhhhhh hhhhhhhh           ss
3h0lH           s     ssss sssss      hhhhhhhhhh hhhhhhhh           ss


TARGET    198   RVDANISVHH P-GEPLGVRT EVKNLNSLRF LAKAIDYEIQ RQITELENGG
3h0lH     193   rcdinvsirp kgskefgtrv eiknvnsfrf vqkaleyeie rqinvveegg
                                                                      
TARGET          sssssssss           s sss    hhh hhhhhhhhhh hhhhhhh   
3h0lH           ssssssssss s        s sss    hhh hhhhhhhhhh hhhhhhh   


TARGET    247   EILNETRSFD YKLGCTMPMR DKEGKQDYRF MPEPNLPPLV LYDDTSLPRG
3h0lH     243   evvqetrtfd pqtgktypmr tkeeaedyry fpdpdlvplk vkkew-----
                                                                      
TARGET              ssssss     sss               sss     ss s ssssssss
3h0lH               ssssss     sss               sss     ss s hhh     


TARGET    297   ADSQQVINID QLRDMLPELP SATRERLVQQ YGMLPEHSFA LLNEVGLLEF
3h0lH     288   --------ie eikknmpelp dqrferlike yglseyeagi lvnhkevgdf
                                                                      
TARGET            ssssssss hhhh     h hhhhhhhhhh     hhhhhh hh   hhhhh
3h0lH                   hh hhhh     h hhhhhhhhhh     hhhhhh hh   hhhhh


TARGET    347   FQNVIKETRT EPKKVTNWVL NTFLCYLKQQ NLAVSESPVT PSALAELLNL
3h0lH     330   feeavrhfk- epkgivnwli ndllgllrdk gisieespvk pehlaelvkl
                                                                      
TARGET          hhhhhhh     hhhhhhhhh    hhhhhhh            hhhhhhhhhh
3h0lH           hhhhhhh     hhhhhhhhh    hhhhhhh            hhhhhhhhhh


TARGET    397   LDRKAISSSA AKQVFEELWK GEGKTAAQIV SEQQL                
3h0lH     379   ikekvistki gkevikemve -tgktpsqiv eekgl-               
                                                                      
TARGET          hhh    hhh hhhhhhhhh       hhhhh hh                   
3h0lH           hhh    hhh hhhhhhhhhh  h   hhhhh hh

Quality 


Template's ligands section 
Ligands in the template: ADP: 1, MG: 1, ZN: 1. 
Ligands in the template that will be assessed: ADP703, MG803, ZN903. 
Model's ligands section 
ADP703 
Not all the residues interacting with the ligand are completely conserved between model and template. 
No RMSD calculation will be performed. 
Given the properties calculated previously, the ligand H.ADP703 will not be included in the model. 
ADP703: conservation:False, RMSD:False, included: False 
 
MG803 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.090 
Given the properties calculated previously, the ligand H.MG803 will be included in the final model. 
MG803: conservation:True, RMSD:True, included: True 
 
ZN903 
Not all the residues interacting with the ligand are completely conserved between model and template. 
No RMSD calculation will be performed. 
Given the properties calculated previously, the ligand H.ZN903 will not be included in the final model. 
ZN903: conservation:False, RMSD:False, included: False 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 3h0l is annotated as HETERO TRIMER 
 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: 3h0l.pdb3.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3h0l_3

Template Selection 
 - Start SMR-Pipeline for:a29748167f85962b1155212ccd4434e9 on BC2-cluster at Fri Feb 22 22:06:57
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
 - No template with M found
 - No template with O found
 - No template with P found
 - No template with R found
 - No template with A found
 - No template with C found
 - No template with S found
 - No template with U found
 - No template with D found
 - No template with F found
 - No template with V found
 - No template with X found
 - No template with G found
 - No template with I found
 - No template with J found
 - No template with L found
 - No template with A found
 - No template with C found
 - No template with A found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with C found
 - No template with M found
 - No template with O found
 - No template with P found
 - No template with R found
 - No template with A found
 - No template with C found
 - No template with S found
 - No template with U found
 - No template with D found
 - No template with F found
 - No template with V found
 - No template with X found
 - No template with G found
 - No template with I found
 - No template with J found
 - No template with L found
 - No template with A found
 - No template with C found
 - No template with G found
 - No template with I found
 - No template with J found
 - No template with L found
 - No template with M found
 - No template with O found
 - No template with P found
 - No template with R found
 - No template with A found
 - No template with C found
 - No template with S found
 - No template with U found
 - No template with D found
 - No template with F found
 - No template with V found
 - No template with X found
 - No template with A found
 - No template with C found
 - No template with A found
 - No template with A found
 - No template with C found
 - No template with C 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 3h0lH (62-492) was successful 
 -          ***********************************************************************
 - building model based on 3al0B (62-555) 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:a29748167f85962b1155212ccd4434e9 on BC2-cluster at Fri Feb 22 22:12:04
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.