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 KKWI THEHNRYRRM VPASDMNM-- LYWSDELAAS AQRHADTCDF
2ddbB 2 kkny--qkei vdkhnalrrs vkptarnmlq mkwnshaaqn akrwadrctf
TARGET hhh hhhhhhhh sssshhhhhh hhhhhh
2ddbB h hhhh hhhhhhhh sss ssshhhhhh hhhhhh
TARGET 43 RHSRGRIN-- ----VGENIW AA--PYSNYS DAISIWFNEV HNPRCGCN-H
2ddbB 50 ahsppntrtv gklrcgenif mssqpfp-ws gvvqawydei knfvygigak
TARGET sssss ss hhhhhhhhhh
2ddbB sss ssssssss ss hh hhhhhh h sss sss
TARGET 84 AYKHCCGHYV QVVWAKTNLV GCGFSRCRDV QGVWGRGHRN VFVCHYNPQG
2ddbB 99 ppgsvighyt qvvwykshli gcasakcss- -------sky lyvcqycpag
TARGET hhhh hh sss ssssssssss ss ssssss sssssss
2ddbB hhhh hhh sss sssssss ss sssssss
TARGET 134 NTVFVTARGQ LYAMPAFTWA SGDNGKCSNC PANAPACYQG LCYMPKNY -
2ddbB 141 ni-----rgs i----atpyk sgp--pcadc ps---acvnr lctnpcnynn
TARGET sss sss
2ddbB s ss sss sss
TARGET ---------- ---------- ---------- ----
2ddbB 177 dfsnckslak kskcqtewik kkcpascfch nkii
TARGET
2ddbB hhhhhh hh hhhh h hhh
Template's ligands section
Ligands in the template:FMT : 3,NA : 1.
Ligands in the template that will be assessed: NA303.
Model's ligands section
NA303
One or more ligand's atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other ligands.
Given the properties calculated previously, the ligand NA303 will not be included in the final model.
NA303: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2ddb is annotated as MONOMER
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: 2ddb.pdb2.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 (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.338 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:6b269304473ec06f6907f8943a857d7c on BC2-cluster at Wed Feb 20 10:11:40
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:1): model based on new templates
- Send 1 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- **********************************************
- building model based on 2ddbB (81-261) 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:6b269304473ec06f6907f8943a857d7c on BC2-cluster at Wed Feb 20 10:13:27
2013
Template Search
| Template Description |
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4ifa: 1.5 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF AN EXTRACELLUCONTAINING A SCP DOMAIN FROM BACILLUS ANTHRACIS STR. AMES Solved by: X-RAY, Resolution: 1.50A, 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.