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 EAEIVYPI TCGDSRANLI WRKFVCPGIN VKCVQYDEHV ISPKEFVHLA
1oqj_1#8 90 dmeiaypi tcgeskaill wkkfvcpgin vkcvkfndql ispkhfvhla
TARGET sssss ss ssssss s ssss ss s hhhhhhhh
1oqj_1#8 sssss ss ssssss s ssss ss s hhhhhhhh
TARGET 49 GKSTLKDWKR AIRMNGIMLR KIMDSGELDF YQHDKVCSNT CR
1oqj_1#8 138 gkstlkdwkr airlggimlr kmmdsgqidf yqhdkvcsnt cr-
TARGET hhh h h hhhh
1oqj_1#8 hhh h h hhhh
Template's ligands section
Ligands in the template:ZN : 1.
Ligands in the template that will be assessed: ZN1.
Model's ligands section
ZN1
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: 0.040
Given the properties calculated previously, the ligand z.ZN1 will be included in the final model.
ZN1: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
1oqj 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: 1oqj.pdb1.gz
Quaternary Structure Modelling of the Target Protein
The quaternary structure can be assumed to be identical
Model was succesfully built as MONOMER.
Template Selection
- Start SMR-Pipeline for:d6cf0b46dad331ab06085fa7e4dd6308 on BC2-cluster at Fri Feb 22 18:49:53
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 1
- But still uncovered regions of the target sequence detected, go for: HHSEARCH
- Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
- Warning: Oligomer Prediction was not successfull!
- 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
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- **************
- building model based on 1oqjA (87-176) 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:d6cf0b46dad331ab06085fa7e4dd6308 on BC2-cluster at Fri Feb 22 18:50:48
2013
Template Search
| Template Description |
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1oqj: CRYSTAL STRUCTURE OF THE SAND DOMAIN FROM GLUCOCORTICOID MODULATORY ELEMENT BINDING PROTEIN-1 (GMEB1) Solved by: X-RAY, Resolution: 1.55A, 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.