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 VD IGSNGIRFSI SSKAAHHARI MPCVFKDRVG LSLYEVQYNT
1t6dA 8 ixrvas--id igsysvrlti aq--ikdgkl siilergri- -----tslgt
TARGET ss ss ssssss ss ssssssss
1t6dA sssss ss ss sssssss ss ss ss sssssssss s
TARGET 43 HTNAKCPIPR DIIKEVCSAM KRFKLICDDF GVPETSVRVI ATEATRDAIN
1t6dA 48 kvketgrlqe drieetiqvl keykklidef kver--xkav ateairrakn
TARGET hhhh h hhhhhhhhhh hhhhhhhhhh sss ss hhh
1t6dA hhhh h hhhhhhhhhh hhhhhhhhhh s ssss ss hhh
TARGET 93 ADEFVNAVYG STGWKVEILG QEDETRVGIY GVVSSFNTVR -GLYLDVAGG
1t6dA 96 aeeflervkr evglvvevit peqegryayl avayslkpeg evxvvdqggg
TARGET hhhhhhhhhh hh sss hhhhhhhhhh hhhhh s sssssss
1t6dA hhhhhhhhhh hh sss hhhhhhhhhh hhhhh ssssssss
TARGET 142 STQLSWVISS HGEVKQSSKP VSLPYGAGTL LRRMR----- TDDNRALFYE
1t6dA 146 steyvf---- -gkgykvrev islpigivnl tetffkqdpp teeevkrffe
TARGET ssssssssss sssss sss hhhh h hhhhhhh
1t6dA ssssss ss sssss sss hhhh hhhh hhhhhhhhh
TARGET 187 IKEAYKDAIE KIGIPQEMID DAKKEGGFDL WTRGGGLRGM GHLLLYQSEG
1t6dA 191 fle---kels kvkkpvdtiv gl-------- ---ggtittl a-aleynvyp
TARGET hh hh sss ss sssss sssss hhhh
1t6dA hhh hhhh sss ss hhhhhh h hhh
TARGET 237 YPIQTIINGY ACTYEEFSSM SDYLFLKQKI PGSSKEHKIF KVSDRR-ALQ
1t6dA 226 ydpqk-vhgk vltygqikkw fdtf---kei pseerskrfr qvedrrakvi
TARGET s ss hhhhhhh hhh hhhhhhh h
1t6dA s ss hhhhhhh hhhh h hhhhhhh hhhhhhh
TARGET 286 LPAVGLFMS- -AVFEAIPQI KAVHFSEGGV REGSLYSLLP KE
1t6dA 272 lagigiflkt leife----- kdlivsdwgl regvlvsexl ken
TARGET hhhhhhhh ssss h hhhhhhhhhh hh
1t6dA hhhhhhhhhh hhhh ssss h hhhhhhhhhh hh
Template's ligands section
Ligands in the template:ALA : 1,TRS : 1.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1t6d 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: 1t6d.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 (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.278 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:e7b5b0cb7ec464c08767584616f1399c on BC2-cluster at Mon Feb 18 21:27:38
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
- 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 3hi0A (21-445) was not successful go to next best template
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- building model based on 3hi0B (21-445) was not successful go to next best template
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- building model based on 1t6dA (22-346) 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:e7b5b0cb7ec464c08767584616f1399c on BC2-cluster at Mon Feb 18 21:31:38
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.