SWISS-MODEL Repository 
Uniprot features:
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 ] |
Alignment
TARGET 1 VTRQII SSANAPGAIG PYSQAVRAGN TIYLSGSLGL DPKTGD-LKE
1oniA 2 ss--lirrvi stakapgaig pysqavlvdr tiyisgqigm dpssgqlvsg
TARGET sss sssss s sssss
1oniA sss sssss s sssss ss s sss
TARGET 46 GVVEQTHQSL KNLGEVLKAA GADYGNVVKT TVLLQNIADF AAVNEVYGQY
1oniA 50 gvaeeakqal knmgeilkaa gcdftnvvkt tvlladindf ntvneiykqy
TARGET hhhhhhhhh hhhhhhhhh sssss sssss hhhhhhhh
1oniA hhhhhhhhh hhhhhhhhhh sssss sssss hhhhhhhhhh
TARGET 96 FKSPYPARAA YQVAALPKGG LVEIEAVAIA GEI ----
1oniA 100 fksnfparaa yqvaalpkgs rieieavaiq gplttasl
TARGET ssss sss ssssssssss
1oniA ssss sss ssssssssss
Template's ligands section
Ligands in the template:BEZ : 2.
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
1oni 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: 1oni.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 (=TRIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.478 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1oniB 1oniC
Template Selection
- Start SMR-Pipeline for:00d42366f37f75314da4a2d43b85573f on BC2-cluster at Mon May 6 07:14:14
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 1 go for
modeling ...
- No A3m found
- 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 1oniA (39-166) 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:00d42366f37f75314da4a2d43b85573f on BC2-cluster at Mon May 6 07:15:07
2013
Template Search
| Template Description |
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1oni: CRYSTAL STRUCTURE OF A HUMAN P14.5, A TRANSLATIONAL INHIBITOR REVEALS DIFFERENT MODE OF LIGAND BINDING NEAR THE INVARIANT RESIDUES OF THE YJGF/UK114 PROTEIN FAMILY Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST |
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1nq3: CRYSTAL STRUCTURE OF THE MAMMALIAN TUMOR ASSOCIATED ANTIGEUK114 Solved by: X-RAY, Resolution: 2.20A, Identified by BLAST |
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1qah: CRYSTAL STRUCTURE OF PERCHLORIC ACID SOLUBLE PROTEIN-A TRANSLATIONAL INHIBITOR Solved by: X-RAY, Resolution: 1.80A, Identified by BLAST |
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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.