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 2012-10-15. 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 FKASRTID WDGMAKVLVT DEARREFSNL RRAFDEVNTQ LQTKFSQEPE
2clyB 4 klalktid wvafgeiipr nq-kavansl kswnetltsr la-tlpekpp
TARGET hhhhh hhhhh hhhhhhhhhh hhh
2clyB hhhhh hhhhhhh hhhhhhhhhh hh h
TARGET 49 PIDWDYYRKG IG-AGIVDKY KEAYDSIEIP KYVDKVTPEY KPKFDALLVE
2clyB 50 aidwayykan vakaglvddf ekkfnalkvp ipedkytaqv daeekedvks
TARGET hhhhhhh hhhhh hhhh hh hhhhhhhhhh
2clyB hhhhhh hhhhh hhhh hh hhhh hh
TARGET 98 LKEAEQKSLK ESERLEKEIA DVQE
2clyB 100 caefltqskt riqeyekele kmrn-
TARGET hhhhhhhhhh hhhhhhhhhh hh
2clyB hhhhhhhh hhhhhhhhhh hh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2cly 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: 2cly.pdb1.gz
Quaternary Structure Modelling of the Target Protein
2cly_1
Template Selection
- Start SMR-Pipeline for:4424e0974f24129ee7eb62404eff6bff on BC2-cluster at Wed Oct 31 17:02:03
2012
- 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:
- No template with A found
- No template with C found
- No template with D found
- No template with F found
- Warning: Oligomer Prediction was not successfull!
- Proof template(s) selection compared to previous Repository update
- Need for modeling since selected templates are the not the same as in previous update
- Send 1 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- **********************************************************
- building model based on 2clyB (13-133) 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:4424e0974f24129ee7eb62404eff6bff on BC2-cluster at Wed Oct 31 17:02:34
2012
Template Search
| Template Description |
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2cly: SUBCOMPLEX OF THE STATOR OF BOVINE MITOCHONDRIAL ATP SYNTHASE Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH |
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4b2q: MODEL OF THE YEAST F1FO-ATP SYNTHASE DIMER BASED ON SUBTOMAVERAGE Solved by: X-RAY, Resolution: 37.00A, 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.