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 STSPYLLH CFELLNLTSR SFAAVIRELH PELRNCVTLF YLILRALDTI
3vj8A 35 slssslkt cykylnqtsr sfaaviqald gemrnavcif ylvlraldtl
TARGET hhhhh hhhhhhhh hhhhhh hhhhhhhh hhhhhhhhhh
3vj8A hhhhh hhhhhhhh hhhhhh hhhhhhhh hhhhhhhhhh
TARGET 49 EDDMSIEHDL KIDLLRHFHE KLLLTKWSFD GNAPDVKDRA VLTDFESILI
3vj8A 83 eddmtisvek kvpllhnfhs flyqpdwrfm eske--kdrq vledfptisl
TARGET hh hhh hhhhh hh h h hh hhhhh
3vj8A hh hhh hhhhh hh hh h hh hhhhh
TARGET 99 EFHKLKPEYQ EVIKEITEKM GNGMADYILD ENYNLNGLQT VHDYDVYCHY
3vj8A 131 efrnlaekyq tviadicrrm gigmaef-ld kh-----vts eqewdkychy
TARGET hhh hhhh hhhhhhhhhh hhhhhhhh sss sss hhhhhhhhhh
3vj8A hhh hhhh hhhhhhhhhh hhhhh hhhhhhhhhh
TARGET 149 VAGLVGDGLT RLIVIAKFAN ESLYSNEQLY ESMGLFLQKT NIIRDYNEDL
3vj8A 175 vaglvgigls rlfsasefed plvgedtera nsmglflqkt niirdyledq
TARGET hhhhhhh hhhhh hhh hhh hhhhhhhhhh hhh hhhh
3vj8A hhhhhhh hhhhh hhh hhh hhhhhhhhhh hhh hhhh
TARGET 199 VDGRSFWPKE IWSQYAPQLK DFMKPENEQL GLDCINHLVL NALSHVIDVL
3vj8A 225 qggrefwpqe vwsryvkklg dfakpenidl avqclnelit nalhhipdvi
TARGET hh hh hhh h hh hhh hhhhhhhhhh hhhhhhhhhh
3vj8A hh hh hhh h hh hh hhhhhhhhhh hhhhhhhhhh
TARGET 249 TYLAGIHEQS TFQFCAIPQV MAIATLALVF NNREVLHGNV KIRKGTTCYL
3vj8A 275 tylsrlrnqs vfnfcaipqv maiatlaacy nnqqvfkgav kirkgqavtl
TARGET hhhh hh hhhhhhhhhh hhhhhhhhh hh hhhhhhh
3vj8A hhhh hh hhhhhhhhhh hhhhhhhhh hh hhhhhhh
TARGET 299 ILKSRTLRGC VEIFDYYLRD IKSKLAVQDP NFLKLNIQIS KI --
3vj8A 325 mmdatnmpav kaiiyqymee iyhripdsdp sssktrqiis tirtq
TARGET hhh hhhh hhhhhhhhhh h hhhhhhhhhh hh
3vj8A hhh hhhh hhhhhhhhhh h hhhhhhhhhh hhhh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3vj8 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: 3vj8.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 0.446 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:b9def4aa9280e95bf4c5ad985918d81d on BC2-cluster at Mon Feb 18 16:59:44
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 3vj8A (34-373) 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:b9def4aa9280e95bf4c5ad985918d81d on BC2-cluster at Mon Feb 18 17:02:07
2013
Template Search
| Template Description |
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4hd1: CRYSTAL STRUCTURE OF SQUALENE SYNTHASE HPNC FROM ALICYCLOBACIDOCALDARIUS Solved by: X-RAY, Resolution: 2.40A, 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.