SWISS-MODEL Repository 
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
Domain
Model 3D Structure
|
|
|
|
|||||||||||||||||||||||||||||||
|
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 ]
|
Alignment
TARGET 1 HAKPPYSY ISLITMAIQN NPTRMLTLSE IYQFIMDLFP FYRQNQQRWQ
1vtn_1#2 117 hakppysy islitmaiqq apgkmltlse iyqwimdlfp yyrenqqrwq
TARGET h hhhhhhhhhh hhh hhhhhhh hh hhhh
1vtn_1#2 h hhhhhhhhh hhh hhhhhhh hh hhhh
TARGET 49 NSIRHSLSFN DCFVKIPRTP DKPGKGSFWT LHPDSGNMFE NGCYLRRQKR
1vtn_1#2 165 nsirhslsfn dcfvkvarsp dkpgkgsywa lhpssgnmfe ngcylrrqkr
TARGET hhhhhhhhh sssss sss ss
1vtn_1#2 hhhhhhhhh sssss sss ss
TARGET 99 FK -
1vtn_1#2 215 fkla
TARGET
1vtn_1#2
Template's ligands section
Ligands in the template:DA : 7,DC : 6,DG : 6,DT : 7,MG : 1.
Ligands in the template that will be assessed: MG30.
Model's ligands section
MG30
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: 0.070
Given the properties calculated previously, the ligand z.MG30 will be included in the final model.
MG30: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
1vtn 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: 1vtn.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:6760349d51af67db2f482a9621a30130 on BC2-cluster at Thu Feb 21 12:14:18
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
FATAL - No A3m found
- Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
- No template with N found
- No template with M found
- No template with N found
- No template with M found
- 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
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ****************
- building model based on 1vtnC (208-307) 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:6760349d51af67db2f482a9621a30130 on BC2-cluster at Thu Feb 21 12:15:16
2013
Template Search
| Template Description |
|
|||||
|
1vtn: CO-CRYSTAL STRUCTURE OF THE HNF-3/FORK HEAD DNA-RECOGNITIORESEMBLES HISTONE H5 Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST |
|
|||||
|
1d5v: SOLUTION STRUCTURE OF THE FORKHEAD DOMAIN OF THE ADIPOCYTETRANSCRIPTION FACTOR FREAC-11 (S12) Solved by: NMR, Identified by BLAST |
|
|||||
|
2hdc: STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX Solved by: NMR, Identified by BLAST |
|
|||||
|
2hfh: THE NMR STRUCTURES OF A WINGED HELIX PROTEIN: GENESIS, 20 STRUCTURES Solved by: NMR, Identified by BLAST |
|
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.