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 ASPH KPWRAEYAKS SRSSCKTCKS VINKENFRLG KLVQSTHFDG
1v9x_1#5 1 gssg--ssgh kpwraeyaks srsscktcks vinkenfrlg klvqsthfdg
TARGET sss sss s ss ss ss
1v9x_1#5 sss sss s ss ss ss
TARGET 45 IMPMWNHASC ILKKTKQIKS VDDVEGIESL RWEDQQKIRK YVESGA ---
1v9x_1#5 49 impmwnhasc ilkktkqiks vddvegiesl rwedqqkirk yvesgagsnt
TARGET sss hhh hh hhhhhhhh
1v9x_1#5 sss hhh hh hhhhhhhh
TARGET ---------- ------
1v9x_1#5 99 ststgtstss sgpssg
TARGET
1v9x_1#5
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: 0.050
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
1v9x is annotated as MONOMER
The template structure (1v9x) was solved by NMR and does not contain any quaternary structure annotation
The template is annotated by the number of chains found in the PDB file
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:85a972951f2d4a5e0cb2afb8378cc2f6 on BC2-cluster at Tue Feb 19 06:27:52
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 md5 found in hash for: 2m2iA
FATAL - No md5 found in hash for: 2m2iA
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:5): model based on new templates
- Send 5 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *******
- building model based on 1v9xA (2-91) was successful
- ****************************
- building model based on 2rd6A (634-982) was successful
- ***************************************
- building model based on 4dqyC (500-982) was successful
- **********
- building model based on 2jvnA (246-365) was successful
- *******
- building model based on 4id3A (398-485) 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:85a972951f2d4a5e0cb2afb8378cc2f6 on BC2-cluster at Tue Feb 19 06:32:36
2013
Template Search
| Template Description |
|
||||||||||
|
1v9x: SOLUTION STRUCTURE OF THE FIRST ZN-FINGER DOMAIN OF POLY(ADP-RIBOSE) POLYMERASE-1 Solved by: NMR, Identified by BLAST |
|
||||||||||
|
4id3: CRYSTAL STRUCTURE OF THE BRCT DOMAIN OF S. CEREVISIAE REV1 Solved by: X-RAY, Resolution: 1.97A, Identified by HHSEARCH |
|
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.