SWISS-MODEL Repository - Model Details

Model Overview
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1
1637

Sequence
UniProt Q9W1B0
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9W1B0: 7227.FBpp0072194

Domain
Link to: [ InterPro ]
Pkinase
C1_1
Pkinase_C
CNH

Model 3D Structure
Model information:
Modelled residue range: 49 to 434
Based on template: [ 3tku ]  
Sequence Identity [%]: 69%
Model date: 2013-03-01
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3tku): DIMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: EDO: 1, M77: 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                                FSLDY LLDTFIVLYD ECSNSSLRRE
3tkuB     2     sakvrlkkle qllldgpwrn esa--lsvet lldvlvclyt ecshsalrrd
                                                                      
TARGET                                       hhh hhhhhhhhhh h        h
3tkuB            hhhhhhhhh hhhhh             hhh hhhhhhhhhh h         


TARGET    26    KGVSDFLKLS KPFVHIVRKL RLSRDDFDIL KIIGRGAFGE VCVVQMISTE
3tkuB     50    kyvaeflewa kpftqlvkem qlhredfeii kvigrgafge vavvkmknte
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh      sssss sss sss  s sssssss   
3tkuB           hhhhhhhhhh hhhhhhhhhh      sssss sss      s sssssss   


TARGET    76    KVYAMKILNK WEMLKRAETA CFREERDVLV FGDRQWITNL HYAFQDNINL
3tkuB     100   riyamkilnk wemlkraeta cfreerdvlv ngdcqwital hyafqdenhl
                                                                      
TARGET          ssssssssss hhhhh       hhhhhhhhh         ss ssssss sss
3tkuB           ssssssssss hhhhh       hhhhhhhhh h       ss ssssss sss


TARGET    126   YLVMDYYCGG DLLTLLSKFE DKLPEDMAKF YITEMILAIN SIHQIRYVHR
3tkuB     150   ylvmdyyvgg dlltllskfe dklpedmarf yigemvlaid sihqlhyvhr
                                                                      
TARGET          sssss    s sshhhhhh       hhhhhh hhhhhhhhhh hhhh sss  
3tkuB           sssss    s sshhhhhh       hhhhhh hhhhhhhhhh hhhh sss  


TARGET    176   DIKPDNVLLD KRGHVRLADF GSCLRLDKDG TVQSNVAVGT PDYISPEILR
3tkuB     200   dikpdnvlld vnghirladf gsclkmnddg tvqssvavgt pdyispeilq
                                                                      
TARGET               sssss    sssss      sss                      hhhh
3tkuB                sssss    sssss      sss      sss             hhhh


TARGET    226   AMEDGKGRYG TECDWWSLGV CMYEMLYGET PFYAESLVET YGKIMNHQNC
3tkuB     250   amedgmgkyg pecdwwslgv cmyemlyget pfyaeslvet ygkimnheer
                                                                      
TARGET          hh          hhhhhhhhh hhhhhh           hhhh hhhh      
3tkuB           h     sss   hhhhhhhhh hhhhhhh          hhhh hhhh      


TARGET    276   FNLPSQETLN YKVSETSQDL LCKLICIPEN RLGQNGIQDF MDHPWFVGID
3tkuB     300   fqfpshvt-- -dvseeakdl iqrlicsrer rlgqngiedf kkhaffegln
                                                                      
TARGET                         hhhhhh hhh               hhh h         
3tkuB                          hhhhhh h                 hhh h         


TARGET    326   WKNIRQGPAP YVPEVSSPTD TSNFDVDDND VRLTDSIPPS ANPAFSGFHL
3tkuB     347   wenirnleap yipdvsspsd tsnfd----- ---------- ----fsglhl
                                                                      
TARGET                                       sss s      sss     sss  h
3tkuB           h   h                                               hh


TARGET    376   PFIGFTFSLT S -------                                  
3tkuB     397   pfigftftte scfsdrgsl                                  
                                                                      
TARGET          h     sss                                             
3tkuB           h     sss

Quality 


Template's ligands section 
Ligands in the template: EDO: 1, M77: 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 
 3tku is annotated as DIMER 
 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: 3tku.pdb1.gz 
      
 
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 (=DIMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.28 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 3tkuA

Template Selection 
 - Start SMR-Pipeline for:ee5765d3ddf7fc05e59fa5caa3e5275d on BC2-cluster at Thu Feb 28 23:01:33
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Warning: sequence length exceeded the limit of 1500 residues
 - HHsearch profile build is skipped
FATAL - No A3m found

 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -   *******************
 - building model based on 3tkuB (49-434) 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:ee5765d3ddf7fc05e59fa5caa3e5275d on BC2-cluster at Fri Mar  1 15:10:46
2013


Template Description
Match Chain SeqId

3tku: MRCK BETA IN COMPLEX WITH FASUDIL
Solved by: X-RAY, Resolution: 2.15A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

49-434 3tkuA 69%
[Model]
49-434 3tkuB 69%
[Model]

3qfv: MRCK BETA IN COMPLEX WITH TPCA-1
Solved by: X-RAY, Resolution: 2.65A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

49-434 3qfvB 69%
[Model]
49-434 3qfvA 69%
[Model]

4aw2: CRYSTAL STRUCTURE OF CDC42 BINDING PROTEIN KINASE ALPHA (M
Solved by: X-RAY, Resolution: 1.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

44-441 4aw2A 69%
[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.