SWISS-MODEL Repository 
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SWISS-MODEL Repository - Model Details
Model Overview
Sequence
Domain
Model 3D Structure
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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 ]
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Alignment
TARGET 1 RPILLTRH GESMDNVRGR IGGDSVISDS GKLYAKKLAS FVEKRLKSEK
1fbtB 1 rsiylcrh geselnlrgr iggdsglsar gkqyayalan fi--rsqgis
TARGET ssssss hhhh hh hhhhhhhhhh h
1fbtB sssssss hhhh hhhhhhhhh hh hh
TARGET 49 AASIWTSTLQ RTNLTASSIV GFPKVQWRAL DEINAGVCDG MTYEEVKKNM
1fbtB 47 slkvwtshxk rtiqtaeal- gvpyeqwkal neidagvcee xtyeeiqehy
TARGET ssss h hhhhhhh sss hhhhhh
1fbtB ssss h hhhhhhhh sss hhhhhh
TARGET 99 PEEYESRKKD KLRYRYPRGE SYLDVIQRLE PVIIELERQR APVVVISHQA
1fbtB 96 peefalrdqd kyryrypkge syedlvqrle pvixelerqe n-vlvichqa
TARGET hhhhhhh hhhhh h hhhhhh sssss hh
1fbtB hhhhhhh hhhhhh hhhhhh s sssss hh
TARGET 149 VLRALYAYFA DRPLKEIPQI EMPLHTIIEI --------- ------
1fbtB 145 vxrcllayfl dkssdelpyl kcplhtvlkl tpvaygcrve siylnv
TARGET hhhhhhhhhh hhhhhh sss
1fbtB hhhhhhhhhh hhhhhh ssssss sss sssss ssss
Template's ligands section
Ligands in the template:PO4 : 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
1fbt 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: 1fbt.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 0.318 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1fbtA
Template Selection
- Start SMR-Pipeline for:2df9e83a620c438f66099a10408bfafb on BC2-cluster at Wed Feb 20 03:52:33
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:
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:3): model based on new templates
- Send 3 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *******************
- building model based on 1fbtB (551-728) was successful
- *****************************************
- building model based on 2axnA (345-728) was successful
- ****************
- building model based on 3cr8A (316-461) 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:2df9e83a620c438f66099a10408bfafb on BC2-cluster at Wed Feb 20 04:02:53
2013
Template Search
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2rgx: CRYSTAL STRUCTURE OF ADENYLATE KINASE FROM AQUIFEX AEOLICUIN COMPLEX WITH AP5A Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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3sr0: CRYSTAL STRUCTURE OF THE PHOSPHORYL TRANSFER TRANSITION STTHE ADENYLATE KINASE: ADP/ALF4/AMP IN THE ACTIVE SITE Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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2rh5: STRUCTURE OF APO ADENYLATE KINASE FROM AQUIFEX AEOLICUS Solved by: X-RAY, Resolution: 2.48A, Identified by HHSEARCH |
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3cr8: HEXAMERIC APS KINASE FROM THIOBACILLUS DENITRIFICANS Solved by: X-RAY, Resolution: 2.95A, Identified by HHSEARCH |
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4gp7: POLYNUCLEOTIDE KINASE Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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4gp6: POLYNUCLEOTIDE KINASE Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH |
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4hbz: THE STRUCTURE OF PUTATIVE PHOSPHOHISTIDINE PHOSPHATASE SIXNAKAMURELLA MULTIPARTITIA. Solved by: X-RAY, Resolution: 1.55A, Identified by HHSEARCH |
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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.