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 DLRYKLMK LVRQKFVMND SLNQTIYQDV DKHYLSTTWL NDLQQEVKFD
2kkiA 9 nvkynfmr iikyefilnd alnqsiiran dq-yltaaal hnldeavkfd
TARGET ssss sss sss sssss sssss sss
2kkiA sssss sssss sss sssss sssss sss
TARGET 49 MYAYSSGGDD SKYPVTLKIS DSQLFVSAQG EDQPVLLKEL PETPKLITGS
2kkiA 56 mgayksskdd akitvilris ktqlyvtaqd edqpvllkem peipktitgs
TARGET sssss sssssss sss sss sss
2kkiA sssss sssssss sss sss sss
TARGET 99 ETDLIFFWKS INSKNYFTSA AYPELFIATK EQSRVHLARG LPSMTDFQI
2kkiA 106 etnllffwet hgtknyftsv ahpnlfiatk qdywvclagg ppsitdfqil
TARGET hh ssss s ssssss ssss sss ss
2kkiA hh ssss s ssssss ssss sss sss
TARGET ----
2kkiA 156 enqa
TARGET
2kkiA
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2kki is annotated as MONOMER
The template structure (2kki) was solved by NMR and does not contain any quaternary structure annotation
The template is annotated by the number of chains found in the PDB file
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 0.146 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:50214918b1b2a38658b20299967959ea on BC2-cluster at Fri Feb 22 13:14:59
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
- No template with B found
- No template with C found
- 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
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- ********************************************
- building model based on 2kkiA (123-269) 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:50214918b1b2a38658b20299967959ea on BC2-cluster at Fri Feb 22 13:16:11
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.