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 VLYNLSPAE LYEQAIKYEK -----GSFIT
1yggA 4 dlnklvkeln dlgltdvke- -ivynpsyeq lfeeetkpgl egfdkgt-lt
TARGET sss hhh hhhhhh
1yggA hhhhhhhhh hh s ssss hhh hhhhhh s ss
TARGET 25 SNGALATLSG AKTGRAPRDK RVVRDATTED ELWWGKGSP- --NIEMDEHT
1yggA 51 tlgavavdtg iftgrspkdk yivcdettkd tvwwnseaak ndnkpmtqet
TARGET sss ss ssss hhh sss hhh
1yggA ssss ss ssss hhhh sss hhh
TARGET 72 FMVNRERAVD YLNSLEKVFV NDQYLNWDPE NRIKVRIVSA RAYHSLFMHN
1yggA 102 wkslrelvak qlsg-krlfv vegycgasek hrigvrmvte vawqahfvkn
TARGET hhhhhhhhhh h sss sssss sssssss hhhhhhhh
1yggA hhhhhhhhhh hh sss sssss sssssss hhhhhhhh
TARGET 122 MCIRPTQEEL ESFGTPDFTI YNAGQFPCNR YTH---YMTS STSVDLNLAR
1yggA 151 mfirptdeel knf-kadftv lngak--ctn pnwkeqglns enfvafnite
TARGET h hhhh sss sss sssss
1yggA h hhhh sss sss hhhh sssss
TARGET 169 REMVILGTQY AGEMKKGLFS VMHYLMPKRR ILSLHSGCNM GKDGDVALFF
1yggA 198 giqliggtwy ggemkkgmfs mmnyflplkg vasmhcsanv gkdgdvaiff
TARGET ssssss hhhhhhhhh hhhhhhh sssssssss s ssssss
1yggA ssssss hhhhhhhhh hhhhhhhhh sssssssss s ssssss
TARGET 219 GLSGTGKTTL STDHNRYLIG DDEHCWTETG VSNIEGGCYA KCVDLSREKE
1yggA 248 glsgtgkttl stdpkrqlig ddehgwdesg vfnfeggcya ktinlsqene
TARGET hhhh h ssss sssssss s ssss sssss ss
1yggA hhhh h ssss sssssss s ssss sssss ss
TARGET 269 PDIWNAIKFG TVLENVVFDE HTREVDYSDK SVTENTRAAY PIEFIPNAKI
1yggA 298 pdiygairrd allenvvv-r adgsvdfddg sktentrvsy piyhidnivr
TARGET hhhhh ssss sssss ss
1yggA hhhhh ssss ss s sss sssss ss
TARGET 319 PC-VGPHPTN VILLACDAFG VLPPVSKLNL AQTMYHFISG YTALVAGTED
1yggA 347 pvskaghatk vifltadafg vlppvskltp eqteyyflsg ftakl-----
TARGET ss sssssss sssss h hhhhhhhhhs ssss
1yggA sss ss sssssss sssss h hhhhhhhhhs ssss
TARGET 368 GIKEPTATFS ACFGAAFIML HPTKYAAMLA EKMKSQGATG WLVNTGWSGG
1yggA 400 ---eptptfs acfgaaflsl hpiqyadvlv ermkasgaea ylvntgwn--
TARGET sssss hhhhhhhh hhhhhh ss ssssssss
1yggA sssss hhhhhhhh hhhhhh ss ssssssss
TARGET 418 SYGVGNRIKL AYTRKIIDAI HSGSLLKANY KKTEIFGFEI PTEIEGIPSE
1yggA 445 --gtgkrisi kdtrgiidai ldgsiekaem gelpifnlai pkalpgvdpa
TARGET sss h hhhhhhhhhh hhhh ss sss sss ss h
1yggA sss h hhhhhhhhhh hhh ss sss sss ss
TARGET 468 ILDPVNSWSD KKAHKDTLVK LGGLFKKNF ---------- -------
1yggA 493 ildprdtyad kaqwqvkaed lanrfvknfv kytanpeaak lvgagpk
TARGET h hh hhhhhhhhh hhhhhhhhh
1yggA hh hhhhhhhhh hhhhhhhhhh h hhhhhh hhh
Template's ligands section
Ligands in the template:NA : 1,SO4 : 2.
Ligands in the template that will be assessed: NA1000.
Model's ligands section
NA1000
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand NA1000 will not be included in the final model.
NA1000: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1ygg 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: 1ygg.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 0.204 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:3c491bc0f98a4bf95bd5d980fb698441 on BC2-cluster at Wed Feb 20 02:03:09
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 1ylhA (151-646) was not successful go to next best template
- ***********************************************************
- building model based on 1yggA (151-646) 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:3c491bc0f98a4bf95bd5d980fb698441 on BC2-cluster at Wed Feb 20 02:07:41
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.