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 ISVIGD EDTCVGFLLG GVGEINKNRH PNFMVVDKNT AVSELEDCFK
2qaiA 2 xk--ivvxgd sdtvvgfrla gv-------h eayeydesle sverarnklr
TARGET ssss hhhhhhhhhh sssss hh hhhhhhhhhh
2qaiA s sssss hhhhhhhhhh sssss hh hhhhhhhhhh
TARGET 47 RFLKRDDIDI ILINQNCAEL IRHVIDAHTS PVPAVLEIPS KDHPYDASKD
2qaiA 42 ellerddvgi iliterlaqr igslpevk-- -fpiilqipd k---fdilrd
TARGET hhhh ss ssssshhhhh h sssss
2qaiA hhh ss ssssshhhhh h sssss hhh
TARGET 97 SILRRA
2qaiA 92 -vvrrai
TARGET hhhh
2qaiA hhhhh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2qai 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: 2qai.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 0.498 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 2qaiB
Template Selection
- Start SMR-Pipeline for:e221357ee54280840c599845cf1bd447 on BC2-cluster at Fri Feb 22 02:47:23
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 2qaiA (12-113) 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:e221357ee54280840c599845cf1bd447 on BC2-cluster at Fri Feb 22 02:48:29
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.