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
3f8tA 18 rigevasrfg lptrvlieiv rtesfqrsla rvtsgkpvvl dlreldsdla
3f8tA hhhhhhhh hhhhhhh hhhhhh h sss ss hhhh
3f8tA 68 swiatharlv epalrelvrt vapdveprvr frglphrfrr verirpmdga
3f8tA hhhh hhh hhhhhhhhhh h sss ss s
3f8tA 118 lisiegvvre vrgaerleha ivdtgselva vrlhghrlgp glrveilgiv
3f8tA ssssssssss ssss sssss ssss ssss sss sssssssss
TARGET 1 DLAK IREVAAREDL YSLLARSIAP
3f8tA 168 rsatldalev hkkdpipevh pdpa--elee freladkdpl -ttfaraiap
TARGET hhh hhhhhh hhhhh
3f8tA s sssssss sss hh hhhh hhhhhh h hhhhhhh
TARGET 25 SIYELEDVKK GILLQLFGGT NKTFTKGGRY RGDINILLCG DPSTSKSQIL
3f8tA 215 -lpgaeevgk mlalqlfscv gknser---- ---lhvllag ypvvc-seil
TARGET hhhhh hhhhhhh sssss hhhh h
3f8tA hhhhh hhhhhhh sssss hhhh hhhh
TARGET 75 QYV-HKITPR GVYTSGKGSS AVGLTAYITR DVDTKQLVLE SGALVLSDGG
3f8tA 256 hhvldhlapr gvyvdlrrte ltdltavlke d---rgwalr agaavladgg
TARGET hhh h s ssssss hhhhssssss s sssss sshhhh s
3f8tA hhhhh s ssssss hhhhssssss s sssss sshhhh s
TARGET 124 VCCIDEFDKM SDSTRSVLHE VMEQQTISIA KAGIITTLNA RSSILASANP
3f8tA 303 ilavdhlega pephrwalme amdkgtvtvd --gi--alna rcavlaainp
TARGET ssssss hhhhhhhhh hhh sss sss ssssss
3f8tA ssssss hhhhhhhhh hhh sssss s ssss ssssss
TARGET 174 IGSRYNPNLP VTENIDLPPP LLSRFDLVYL VLDKVDEKND RELAKHLTNL
3f8tA 349 ----gepsdp piaridldqd flshfdliaf l--------- ----------
TARGET hh hh hhh ssss shhhhhhhhh hhhhhh
3f8tA hh hh hhh ssss s
TARGET 224 YLEDKPEHIS QDDVLPVEFL TMYISY-AKE HIHPIITEAA KTELVRAYVG
3f8tA 378 ---------- --gvpsytll rryllyaire hpapelteea rkrlehwyet
TARGET hhh hhhhhh hh ssshhh hhhhhhhhhh
3f8tA hhhh hhhhhhhhhh ssshhh hhhhhhhhhh
TARGET 273 M-------RK MGDDSRSDEK RITATTRQLE SMIRLAEAHA KMKLKNVVEL
3f8tA 430 rreeveerlg mglpt----- -lpvtrrqle sverlakaha rmrlsddvep
TARGET hhhhh hhhhhhhhhh hhh sss h
3f8tA hhhhhhhhhh h hhhhh hhhhhhhhhh hhh sss h
TARGET 316 EDVQEAVRLI --------
3f8tA 474 edvdiaaelv dwyletamq
TARGET hhhhhhhhhh
3f8tA hhhhhhhhhh hhhhhh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3f8t is annotated as MONOMER
PISA was used to annotate the quaternary structure, because the author assignment was not complete
PISA annotates this structure as Monomer, therefore the corresponding PDB chain was used as template structure
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 0.474 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:c4ee6d3fa3b516ae2d4323f9e5befa11 on BC2-cluster at Mon Feb 18 11:48:32
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
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *****************************************************
- building model based on 3f9vA (209-830) was not successful go to next best template
- ****************************
- building model based on 3f8tA (505-829) was successful
- *********************
- building model based on 2vl6C (209-449) 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:c4ee6d3fa3b516ae2d4323f9e5befa11 on BC2-cluster at Mon Feb 18 11:53:14
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.