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 PIFTG RPFVVAWNVP TQECAPRHKV PLDLRAFDVK ATPNEGFFNQ
2pe4A 20 rsfrgpllpn rpfttvwnan tqwclerhgv dvdvsvfdvv anpgqtfrgp
TARGET sssss hhhhhh ss s
2pe4A sssss hhhhhh ss s
TARGET 46 NITTFYYDRL GLYPRFDAAG TSVHGGVPQN GSLCAHLPML KESVERYIQT
2pe4A 70 dmtifyssql gtypyytptg epvfgglpqn asliahlart fqdilaaipa
TARGET sssssss sss sss hhhhhhhh hhhhhhh
2pe4A sssss sss sss hhhhhhhh hhhhhhh
TARGET 96 QEPGGLAVID WEEWRPVWVR NWQEKDVYRQ SSRQLVASRH PDWPSDRVMK
2pe4A 120 pdfsglavid weawrprwaf nwdtkdiyrq rsralvqaqh pdwpapqvea
TARGET ssssss hhhhhh hhhhhhhhh hhhhhh
2pe4A ssssss hhhhhh hhhhhhhhh hhhhhh
TARGET 146 QAQYEFEFAA RQFMLNTLRY VKAVRPQHLW GFYLFPDCYN HDYVQNWESY
2pe4A 170 vaqdqfqgaa rawmagtlql gralrprglw gfygfpdcyn ydfls--pny
TARGET hhhhhhhhhh hhhhhhhhhh hhhh ss sss
2pe4A hhhhhhhhhh hhhhhhhhhh hhhh ss sss
TARGET 196 TGRCPDVEVA RNDQLAWLWA ESTALFPSVY LDETLASSVH SRNFVSFRVR
2pe4A 218 tgqcpsgira qndqlgwlwg qsralypsiy mpavlegtgk sqmyvqhrva
TARGET hhh hhh hhhh h sss hhhhhhhhhh
2pe4A hhh hh hhhhh h sss hhhhhhhhhh
TARGET 246 EALRVAHTHH ANHALPVYVF TRPTYTRGLT GLSQVDLIST IGESAALGSA
2pe4A 268 eafrva-vaa gdpnlpvlpy vqifydttnh flpldelehs lgesaaqgaa
TARGET hhhhhh sss s sss s ss hhhh hhhhhh s
2pe4A hhhhhh hh sss s sss s ss hhhh hhhhhh s
TARGET 296 GVIFWGDSED ASSMETCQYL KNYLTQLLVP YIVNVSWATQ YCSWTQCHGH
2pe4A 317 gvvlwvswen trtkescqai keymdttlgp filnvtsgal lcsqalcsgh
TARGET ssssss hhhhhhh hhhhh hh hhhhhhhhhh hhhhhh s
2pe4A ssssss hhhhhhh hhhhh hh hhhhhhhhhh hhhhhh s
TARGET 346 GRCVRRNPSA NTFLHLNASS FRLVPG--HT PSEPQLRPEG QLSEADLNYL
2pe4A 367 grcvrrtshp kallllnpas fsiqltpggg p----lslrg alsledqaqm
TARGET ssssss s ssss ssss s hhhhhhh
2pe4A ssssss s ssss ssss s hhhhhhh
TARGET 394 QKHFRCQCYL GWGGEQCQR ----
2pe4A 413 avefkcrcyp gwqapwcerk smwt
TARGET hhsssssss
2pe4A hhsssssss sss ss s
Template's ligands section
Ligands in the template:ACT : 4,GOL : 1,NAG : 2.
Ligands in the template that will be assessed: NAG550, NAG599.
Model's ligands section
NAG550
One or more ligand's atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other ligands.
Given the properties calculated previously, the ligand B.NAG550 will not be included in the model.
NAG550: conservation:False, RMSD:False, included: False
NAG599
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand C.NAG599 will not be included in the model.
NAG599: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2pe4 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: 2pe4.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 0.312 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:97f59e521d59b0c56baea391d84e5f56 on BC2-cluster at Sat Feb 23 00:06:54
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 H found
- No template with L 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
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- **********************************************************************
- building model based on 2pe4A (29-440) 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:97f59e521d59b0c56baea391d84e5f56 on BC2-cluster at Sat Feb 23 00:09:03
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.