SWISS-MODEL Repository - Model Details

Model Overview
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1
1962

Sequence
UniProt P05661
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Myosin_head
Myosin_tail_1
Myosin_N

Model 3D Structure
Model information:
Modelled residue range: 776 to 839
Based on template: [ 1wdc ]  
Sequence Identity [%]: 65%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1wdc): HETERO TRIMER
Model built :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       RDERLGKI MSWMQAWARG YLSRKGFKKL QEQRVALKVV QRNLRKYLQL
1wdcA     774     rderlski ismfqahirg ylirkaykkl qdqriglsvi qrnirkwlvl
                                                                      
TARGET              hhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh
1wdcA               hhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh


TARGET    49    RTWPWYKLWQ KVKPLL                                     
1wdcA     822   rnwqwwklys kvkpll-                                    
                                                                      
TARGET             hhhhhhh hhhh                                       
1wdcA              hhhhhhh hhhh

Quality 


Template's ligands section 
Template without ligands. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 1wdc 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: 1wdc.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 1wdc_1

Template Selection 
 - Start SMR-Pipeline for:9a21635ca189ec113918955b3cd5a371 on BC2-cluster at Thu Feb 21 22:53:03
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

FATAL - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with Y found
 - No template with Z found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with Y found
 - No template with Z found
 - No template with W found
 - No template with X found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with Y found
 - No template with Z found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with F found
 - No template with B found
 - No template with H found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with E found
 - No template with F found
 - No template with B found
 - No template with C found
 - No template with E found
 - No template with F found
 - No template with Y found
 - No template with Z found
 - No template with B found
 - No template with B found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with E found
 - No template with F found
 - No template with B found
 - No template with C found
 - No template with E found
 - No template with F found
 - No template with Y found
 - No template with Z found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with E found
 - No template with F found
 - No template with B found
 - No template with C found
 - No template with E found
 - No template with F found
 - No template with Y found
 - No template with Z found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with F found
 - No template with B found
 - No template with H found
 - No template with D found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:4): model based on new templates
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                 ***
 - building model based on 1wdcA (776-839) was successful 
 -  **********************************
 - building model based on 1qviA (16-839) was successful 
 -  ***********************************
 - building model based on 3j04A (32-893) was successful 
 -                                   *****
 - building model based on 2fxmA (837-962) 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:9a21635ca189ec113918955b3cd5a371 on BC2-cluster at Thu Feb 21 23:04:24
2013


Template Description
Match Chain SeqId

3jtd: CALCIUM-FREE SCALLOP MYOSIN REGULATORY DOMAIN WITH ELC-D19POINT MUTATION
Solved by: X-RAY, Resolution: 2.57A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

776-839 3jtdA 66%
[Model]

1wdc: SCALLOP MYOSIN REGULATORY DOMAIN
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

776-839 1wdcA 66%
[Model]

3jvt: CALCIUM-BOUND SCALLOP MYOSIN REGULATORY DOMAIN (LEVER ARM)WITH RECONSTITUTED COMPLETE LIGHT CHAINS
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

777-839 3jvtA 65%
[Model]

3pn7: VISUALIZING NEW HINGES AND A POTENTIAL MAJOR SOURCE OF COMTHE LEVER ARM OF MYOSIN
Solved by: X-RAY, Resolution: 2.25A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

772-839 3pn7A 65%
[Model]
772-839 3pn7D 65%
[Model]

3tuy: PHOSPHORYLATED LIGHT CHAIN DOMAIN OF SCALLOP SMOOTH MUSCLE
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

772-839 3tuyA 65%
[Model]
772-839 3tuyD 65%
[Model]

3ts5: CRYSTAL STRUCTURE OF A LIGHT CHAIN DOMAIN OF SCALLOP SMOOTMYOSIN
Solved by: X-RAY, Resolution: 2.39A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

772-839 3ts5A 65%
[Model]
772-839 3ts5D 65%
[Model]

1scm: STRUCTURE OF THE REGULATORY DOMAIN OF SCALLOP MYOSIN AT 2.ANGSTROMS RESOLUTION
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

779-838 1scmA 63%
[Model]

1s5g: STRUCTURE OF SCALLOP MYOSIN S1 REVEALS A NOVEL NUCLEOTIDE CONFORMATION
Solved by: X-RAY, Resolution: 3.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

32-838 1s5gA 60%
[Model]

4e7z: MYOSIN VI (MD) PRE-POWERSTROKE STATE, P21 CRYSTAL FORM
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

36-795 4e7zB 31%
[Model]

4anj: MYOSIN VI (MDINSERT2-GFP FUSION) PRE-POWERSTROKE STATE (MG
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

35-839 4anjA 31%
[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.