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 FLTLEGIS APLDKANVDT DAIIPKQFLK TIKRTGLKKG LFYEWRFRKD
3h5eB 4 fhthsgig vplrrsnvdt dqiipavflk rvtrtgfedg lfagwr----
TARGET ss sss h hhh hh ssss
3h5eB sssssss sss h hhh hh hhhh
TARGET 49 DQGKDQETDF VLNVEPWREA EILVVTGDNF GCGSSREHAP WALKDFGIKS
3h5eB 48 -----sdpaf vlnlspfdrg svlv-agpdf gtgssrehav walmdygfrv
TARGET ssss hh ssss hhh hhhhhh ss
3h5eB hh sss ss hhh hhhhhh ss
TARGET 99 IIAPSYGDIF YNNSFKNGLL PIRLDQ --- ---------- ----------
3h5eB 92 vissrfgdif rgnagkagll aaevaqddve ilwklieqsp gleitanlqd
TARGET sss hhh hhhhhhh s ssss
3h5eB sss hhh hhhhhhh s ssss hhhhh hhhhhhhh sssssss
TARGET ---------- ----
3h5eB 142 riitaatvvl pfki
TARGET
3h5eB sssss sss ss
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3h5e 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
The target and template sequences are too diverse (seqid: 46.774) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode
The target structure was calculated as SINGLE CHAIN
Template Selection
- Start SMR-Pipeline for:d4a2e5c2d37506762593564baed0324d on BC2-cluster at Mon Feb 18 17:29:21
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:3): model based on new templates
- Send 3 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *************
- building model based on 3h5eB (548-671) was successful
- ******************
- building model based on 2hcuA (545-724) was successful
- **********************************************************
- building model based on 1c96A (119-681) 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:d4a2e5c2d37506762593564baed0324d on BC2-cluster at Mon Feb 18 17:35:21
2013
Template Search
| Template Description |
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3vba: CRYSTAL STRUCTURE OF METHANOGEN 3-ISOPROPYLMALATE ISOMERASSUBUNIT Solved by: X-RAY, Resolution: 2.00A, 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.