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 LDSG DPNGPLSRAV RNQLRLNGVE LLDKETTRKD VPSLRLGKVS
2r76A 36 nqls--lsss deykeltrlv rerlrlnnvk ivdaan---d vpvlrlitds
TARGET sss hhhhhh hhhhhh sss ss s ssssssss
2r76A ssss ssss hhhhhh hhhhhh s ss sssssssss
TARGET 45 IAKDTASVFR NGQTAEYQMI MTVNATVLIP GRDIYPISAK VFRSFFDNPQ
2r76A 81 lerstlslyp tgnvaeyeli yfvefavalp gkeaqpfkie irrdylddpr
TARGET sssssssss ssssssss ssssssss ssssss sssssss
2r76A sssssssss ssssssss ssssssss ssssss sssssss
TARGET 95 MALAKDNEQD MIVKEMYDRA AEQLIRKLPS ------
2r76A 131 talaksrexe llvkexriqa adrilqsxas tevnleh
TARGET hhhhhhhhh hhhhhhhhhh hhhhhhhhhh
2r76A hhhhhhhhh hhhhhhhhhh hhhhhhhhhh h h
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2r76 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: 2r76.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 0.186 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 2r76B
Template Selection
- Start SMR-Pipeline for:e7ec6a3e31a15a30f8d6904a026cdfe7 on BC2-cluster at Sat Feb 23 12:36:48
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
FATAL - No A3m found
- Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
- 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 2r76A (38-161) 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:e7ec6a3e31a15a30f8d6904a026cdfe7 on BC2-cluster at Sat Feb 23 12:37:54
2013
Template Search
no data available!
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.