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 NRELSIVL APFSGGQGKL GVEKGPKYML KHGLQTSIED LGWSTELEPS
2aebB 5 srtigiig apfskgqprg gveegptvlr kaglleklk- -----eqecd
TARGET ssssss s hh hhhhh h hhhh s
2aebB ssssss s hhhhhhhhhh hhhhhh s
TARGET 49 MDEAQFVGKL KMEKDSTTGG SSVMIDGVKA KRADLVGEAT KLVYNSVSKV
2aebB 47 vkdygdlpfa dipndsp--- ----fqivkn prs--vgkas eqlagkvaev
TARGET ssss h hhh hhhh hhhhhhhhhh
2aebB ssss hhh hhhhh hhhhhhhhhh
TARGET 99 VQANRFPLTL GGDHSIAIGT VSAVLDKYPD AGLLWIDAHA DINTIESTPS
2aebB 88 kkngrislvl ggdhslaigs isgharvhpd lgviwvdaht dintplttts
TARGET hh sssss s hhhhhh hhhhhhh ssssss
2aebB hh sssss s hhhhhh hhhhhhh ssssss sss
TARGET 149 GNLHGCPVSF LMG-LNKDVP HCPESLKWVP GNLSPKKIAY IGLRDVDAGE
2aebB 138 gnlhgqpvsf llkelkgkip dvp-gfswvt pcisakdivy iglrdvdpge
TARGET hhh h ssss sss hhh
2aebB ssshhh h ssss sss hhh
TARGET 198 KKILKDLGIA AFSMYHVDKY GINAVIEMAM KAVHPETNGE GPIMCSYDVD
2aebB 187 hyilktlgik yfsmtevdrl gigkvmeetl syllgrk--k rpihlsfdvd
TARGET hhhhhhh s ss hhhhhh hhhhhhhh hhh ssssssss
2aebB hhhhhhh s ss hhhhhh hhhhhhhh hhh ssssssss
TARGET 248 GVDPLYIPAT GTPVRGGLTL REGLFLVERL AESGNLIALD VVECNPDLAI
2aebB 235 gldpsftpat gtpvvgglty reglyiteei yktgllsgld imevnpslgk
TARGET h hhhhhhhhhh hh sss ss
2aebB h hhhhhhhhhh hh sss ss
TARGET 298 HDIHVSNTIS AGCAIARCAL G -------
2aebB 285 tpeevtrtvn tavaitlacf glaregnhk
TARGET hhhhhhhh hhhhhhhh
2aebB hhhhhhhh hhhhhhhh
Template's ligands section
Ligands in the template:AB5 : 1,MN : 2.
Ligands in the template that will be assessed: MN1362, MN1363.
Model's ligands section
MN1362
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.030
Given the properties calculated previously, the ligand MN1362 will be included in the final model.
MN1362: conservation:True, RMSD:True, included: True
MN1363
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.120
Given the properties calculated previously, the ligand MN1363 will be included in the final model.
MN1363: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
2aeb is annotated as TRIMER
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: 2aeb.pdb2.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 (=TRIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.272 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:c89c50faff250aba83f2b5691b4efa08 on BC2-cluster at Mon Feb 18 20:14:23
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 2aebB (12-329) 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:c89c50faff250aba83f2b5691b4efa08 on BC2-cluster at Mon Feb 18 21:02:10
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.