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 ] |
Alignment
TARGET 1 MKLMIVGN TGSGKTTLLQ QLMKTKKSDL GMQSATVGID VKDWPIQIRD
2zejB 1336 xklxivgn tgsgkttllq qlxkt----- --qsatvgid vkdwpi----
TARGET sssss hhhhhh hhh sss ssssss
2zejB sssss hhhhhh hhh sss ssss
TARGET 49 KRKRDLVLNV WDFAGREEFY STHPHFMTQR ALYLAVYDLS KGQAEVDAMK
2zejB 1388 -----lvlnv wdfagreefy sthphfxtqr alylavydls kgqaevdaxk
TARGET sssss ssss hhhhh hhhhhh sssssss hhhhhhh
2zejB sss ssss hhhhh hhhhhh sssssss hhhhhhh
TARGET 99 PWLFNIKARA SSSPVILVGT HLDVSDEKQR KACMSKITKE LLNKRGFPAI
2zejB 1433 pwlfnikara ssspvilvgt hldvsdekqr kacxskitke llnkrgfpai
TARGET hhhhhhhhh ssssssss s hhhhhhhhh ss
2zejB hhhhhhhhh ssssssss hhhhhhhhh ss
TARGET 149 RDYHFVNATE ESDALAKLRK TIINESLNFK
2zejB 1483 rdyhfvnate esdalaklrk tiineslnfk -
TARGET ssssss hhhhhhhh hhhhhhhhh
2zejB ssssss hhhhhhhh hhhhhhhhh
Template's ligands section
Ligands in the template:GDP : 2,MG : 1.
Ligands in the template that will be assessed: GDP1, GDP2, MG1.
Model's ligands section
GDP2
GDP2 interacts, within a radius of 3 Angstroem, with the following ions: MG1. They will be considered as a single ligand.
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: 0.540
Given the properties calculated previously, the ligand B.GDP2 will be included in the model.
GDP2: conservation:True, RMSD:True, included: True
GDP1
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: 0.080
Given the properties calculated previously, the ligand A.GDP1 will be included in the model.
GDP1: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Oligomer Annotation of the Template structure
Sorry, we haven't found any oligomeric annotation for this template.
Either the complex was too large (>60 chains) or the structures was excluded for other reasons.
Please contact help@swissmodel.org for more information!
Template Selection
- Start SMR-Pipeline for:9881e7f1fbeb971605a72097fd1e8f74 on BC2-cluster at Sat May 4 17:47:38
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
- Warning: sequence length exceeded the limit of 1000 residues
- HHsearch profile build is skipped
- No A3m found
- A3m will not be built - sequence too long
- Skipping oligomeric state prediction due to too many templates for cluster: 1335_1508
- Warning: Oligomer Prediction was not successfull!
- Warning: clustersMergedFile not 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 2zejB (1335-1512) 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:9881e7f1fbeb971605a72097fd1e8f74 on BC2-cluster at Sat May 4 17:48:08
2013
Template Search
| Template Description |
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2zej: STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S DISEASE- ASSOCIATED LEUCINE-RICH REPEAT KINASE 2 REVEALS A DIMERICGTPASE Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST |
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3d6t: STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S DISEASE- ASSOCIATED LEUCINE-RICH REPEAT KINASE 2 REVEALS A DIMERICGTPASE Solved by: X-RAY, Resolution: 2.43A, 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.