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 SNCVPR HVGFIMDGNR RFARKKEMDV KEGHEAGFVS MSRILELCYE
4h8e_1#3 19 ld--ssnipe hiaiimdgng rwakkrkmpr ikghyegmqt ikkitriasd
TARGET s sssss hh hhhhhh hhhhhh h hhhhhhhhhh
4h8e_1#3 s sssss hh hhhhhh hhhhhhhhhh hhhhhhhhhh
TARGET 47 AGVDTATVFA FSIENFKRSS REVESLMTLA RERIRQITER GELACKYGVR
4h8e_1#3 67 igvkyltlya fstenwsrpe sevnyimnlp vnflk--tfl peliek-nvk
TARGET h sssssss hhh h hhhhhhhhhh hhh h hhhhhh s
4h8e_1#3 h sssssss h hhhhhhhhhh hhhhh hhh hhhhhh s
TARGET 97 IKIIGDLSLL DKSLLEDVRV AVETTKNNKR ATLNICFPYT GREEILHAMK
4h8e_1#3 114 vetigftdkl pkstieainn akektanntg lklifainyg graelvhsik
TARGET ssss hhhhhhhhh hhhh sssssss hhhhhhhhhh
4h8e_1#3 ssss hhhhhhhhh hhhh sssssss hhhhhhhhhh
TARGET 147 ETIVQH-KKG AA---IDEST LESHLYTAGV PPLDLLIRTS GVSRLSDFLI
4h8e_1#3 164 nmfdelhqqg lnsdiidety innhlmtkdy pdpellirts geqrisnfli
TARGET hhhhh hhh hhh sssssss
4h8e_1#3 hhhhhhhhh hhh hhh sssssss
TARGET 193 WQASSKGVRI ELLDCLWPEF --------- ---------- ------ SNC
4h8e_1#3 214 wqvsysefif n--qklwpdf -dedelikci kiyqsrqrrf gglld--ssn
*
TARGET ssss s
4h8e_1#3 ssss s hhhhhhhh hhhh
TARGET 216 VPRHVGFIMD GNRRFARKKE MDVKEGHEAG FVSMSRILEL CYEAGVDTAT
4h8e_1#3 24 ipehiaiimd gngrwakkrk mprikghyeg mqtikkitri asdigvkylt
TARGET ssssss hhhhhhhh hhhhhh hhhhhhhh hhhh ssss
4h8e_1#3 ssssss hhhhhhhh hhhhhhh hhhhhhhhhh hhhh ssss
TARGET 266 VFAFSIENFK RSSREVESLM TLARERIRQI TERGELACKY GVRIKIIGDL
4h8e_1#3 74 lyafstenws rpesevnyim nlpvnflk-- tflpeliek- nvkvetigft
TARGET sss hhh hhhhhhhh hhhhhh hhhhhhh sssss
4h8e_1#3 sss hhhhhhhh hhhhhhhh hhhhhhhhh sssss
TARGET 316 SLLDKSLLED VRVAVETTKN NKRATLNICF PYTGREEILH AMKETIVQH-
4h8e_1#3 121 dklpkstiea innakektan ntglklifai nyggraelvh siknmfdelh
TARGET hhhhhh hhhhhhh sssssss hhhhhhh hhhhhhhh
4h8e_1#3 hhhhhh hhhhhhh sssssss hhhhhhh hhhhhhhhhh
TARGET 365 KKGAA---ID ESTLESHLYT AGVPPLDLLI RTSGVSRLSD FLIWQASSKG
4h8e_1#3 171 qqglnsdiid etyinnhlmt kdypdpelli rtsgeqrisn fliwqvsyse
TARGET hhhhhh ssss sss s
4h8e_1#3 hh hhhhhh ssss sss s
TARGET 412 VRIELLDCLW PEF ------ ---------- -----
4h8e_1#3 221 fifn--qklw pdfdedelik cikiyqsrqr rfggl
TARGET ssss
4h8e_1#3 ssss hhhhhh hhhhhh
Template's ligands section
Ligands in the template:FPP : 2,MG : 2,SO4 : 2.
Ligands in the template that will be assessed: MG1, MG138.
Model's ligands section
MG1
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand z.MG1 will not be included in the final model.
MG1: conservation:False, RMSD:False, included: False
MG138
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand z.MG138 will not be included in the final model.
MG138: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
4h8e is annotated as DIMER
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: 4h8e.pdb1.gz
Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template can be assumed to be similar (=DIMER)
The corresponding reliability score is 0.842 (>0.5 indicates similarity)
Model was succesfully built as DIMER.
Template Selection
- Start SMR-Pipeline for:3396cccdd82d8a79bbdbd6caead06dee on BC2-cluster at Tue Feb 19 00:07:54
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- 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 4h8eA (28-239) 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:3396cccdd82d8a79bbdbd6caead06dee on BC2-cluster at Tue Feb 19 00:15:56
2013
Template Search
| Template Description |
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4h8e: STRUCTURE OF S. AUREUS UNDECAPRENYL DIPHOSPHATE SYNTHASE IWITH FPP AND SULFATE Solved by: X-RAY, Resolution: 1.30A, Identified by HHSEARCH |
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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.