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 NEAENG SIAEAMEYLT NILSTKVYDI AIESPLQLAK
3iauB 20 ilpkvvpgel iv--nkptgg dsdelfqylv dilaspvydv aiesplelae
TARGET hhhhhhhhh hhhh sssssh
3iauB ss s hhhhhhhhh hhhh sssssh
TARGET 37 KLSKRLGVRM YLKREDLQPV FSFKLRGAYN MMVKLPADQL AKGVICSSAG
3iauB 68 klsdrlgvnf yikredkqrv fsf-lrgayn mmsnlsreel dkgvitasag
TARGET hhhhhh ss sssss hhhh hhh hhhh hh sssss
3iauB hhhhhh ss sssss sss hhhhh hhh hhhh hh sssss
TARGET 87 NHAQGVALSA SKLGCTAVIV MPVTTPEIKW QAVENLGATV VLFGDSYDQA
3iauB 118 nhaqgvalag qrlncvakiv mptttpqiki davralggdv vlygktfdea
TARGET hhhhhhhhhh hhh sssss s hhh hhhhh ss sss hhhh
3iauB hhhhhhhhhh hhh sssss s hhh hhhhh ss sss hhhh
TARGET 137 QAHAKIRAEE EGLTFIPPFD HPDVIAGQGT VGMEITRQAK GPLHAIFVPV
3iauB 168 qthalelsek dglkyippfd dpgvikgqgt igteinrqlk d-ihavfipv
TARGET hhhhhhhhhh h hhhhhhhhh hhhhhhhh sssssss
3iauB hhhhhhhhhh h hhhhhhhhh hhhhhhhh sssssss
TARGET 187 GGGGLIAGIA AYVKRVSPEV KIIGVEPADA NAMALSLHHG ERVILDQVGG
3iauB 217 ggggliagva tffkqiapnt kiigvepyga asmtlslheg hrvklsnvdt
TARGET hhhhhhh hhhhhh ssssssss hhhhhhhh
3iauB hhhhhhh hhhhhh ssssssss hhhhhhhh
TARGET 237 FADGVAVKEV GEETFRISRN LMDGVVLVTR DAICASIKDM FEEKRNILEP
3iauB 267 fadgvavalv geytfakcqe lidgmvlvan dgisaaikdv ydegrnilet
TARGET hhhhhhhhh sssss h hhhhhhhhhh hhh h
3iauB hhhhhhhhh ssssss h hhhhhhhhhh hhh h
TARGET 287 AGALALAGAE AYCKYYGLKD VNVVAITSGA NMNFDKLRIV TELANV
3iauB 317 sgavaiagaa aycefykikn enivaiasga nmdfsklhkv telagl-
TARGET h hhhhhh hhhhhh sssssss hhhhhh hhhh
3iauB h hhhhhh hhhhhh ssssssssss hhhhhh hhhh
Template's ligands section
Ligands in the template:ACT : 1,ALA : 1.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3iau 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: 3iau.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 (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.18 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:4ac71373e85eb92f6dbea718c7df4d0a on BC2-cluster at Wed Feb 20 02:30:17
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:
- No template with B found
- No template with A found
- No template with A found
- No template with B found
- No template with D found
- No template with B found
- No template with B found
- No template with A found
- 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 3iauB (82-413) was successful
- **************************************************
- building model based on 3iauA (48-414) was successful
- ***************************************************************
- building model based on 1tdjA (91-558) was not successful go to next best template
- 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:4ac71373e85eb92f6dbea718c7df4d0a on BC2-cluster at Wed Feb 20 04:10:34
2013
Template Search
| Template Description |
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3iau: THE STRUCTURE OF THE PROCESSED FORM OF THREONINE DEAMINASEISOFORM 2 FROM SOLANUM LYCOPERSICUM Solved by: X-RAY, Resolution: 2.35A, Identified by BLAST |
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4i1y: THE STRUCTURE OF CYSTEINE SYNTHASE FROM MYCOBACTERIUM ULCE Solved by: X-RAY, Resolution: 2.60A, 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.