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 KFKLVFLG EQSVGKTSII TRFMYDSFDN TYQATIGIDF LSKTMYLEDR
2gilB 13 kfklvflg eqsvgktsli trfmydsfdn tyqatigidf lsktmyledr
TARGET ssssss hhhhh hhhh ssss sssss
2gilB ssssss hhhhh hhhh ssss sssss
TARGET 49 TIRLQLWDTA GQERFRSLIP SYIRDSSVAV VVYDITNANS FHQTTKWVDD
2gilB 61 tvrlqlwdta gqerfrslip syirdstvav vvyditnvns fqqttkwidd
TARGET sssssssss hhhh hhhhh sss sssss hh hhhhhhhhhh
2gilB sssssssss hhhh hhhhh sss sssss hh hhhhhhhhhh
TARGET 99 VRNERGCDVI IVLVGNKTDL ADKRQVSTED GEKKARDLNV MFIETSAKAG
2gilB 111 vrtergsdvi imlvgnktdl adkrqvsiee gerkakelnv mfietsakag
TARGET hhhh s sssssss hhh hhhhhhhh sssss
2gilB hhhh s sssssss hh hhhhhhhh sssss
TARGET 149 YNVKQLFRKI ATAL
2gilB 161 ynvkqlfrrv aaal-
TARGET hhhhhhhh hhh
2gilB hhhhhhhh hhh
Template's ligands section
Ligands in the template:GTP : 1,MG : 1.
Ligands in the template that will be assessed: GTP2200, MG2201.
Model's ligands section
GTP2200
GTP2200 interacts, within a radius of 3 Angstroem, with the following ions: MG2201. 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: 0.060
Given the properties calculated previously, the ligand GTP2200 will be included in the model.
GTP2200: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
2gil 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: 2gil.pdb2.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 (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.216 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:9acddb6b4eeba00a841df3aa55612264 on BC2-cluster at Wed Feb 20 12:56:17
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 1 go for
modeling ...
FATAL - No A3m found
- No template with F found
- No template with F found
- No template with D found
- No template with E found
- No template with B 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 2gilB (11-172) 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:9acddb6b4eeba00a841df3aa55612264 on BC2-cluster at Wed Feb 20 12:57:34
2013
Template Search
| Template Description |
|
||||||||||||||||||||
|
2y8e: CRYSTAL STRUCTURE OF D. MELANOGASTER RAB6 GTPASE BOUND TO GMPPNP Solved by: X-RAY, Resolution: 1.39A, Identified by BLAST |
|
||||||||||||||||||||
|
2gil: STRUCTURE OF THE EXTREMELY SLOW GTPASE RAB6A IN THE GTP BOUND FORM AT 1.8 RESOLUTION Solved by: X-RAY, Resolution: 1.82A, Identified by BLAST |
|
||||||||||||||||||||
|
1yzq: GPPNHP-BOUND RAB6 GTPASE Solved by: X-RAY, Resolution: 1.78A, Identified by BLAST |
|
||||||||||||||||||||
|
3bbp: RAB6-GTP:GCC185 RAB BINDING DOMAIN COMPLEX Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST |
|
||||||||||||||||||||
|
3cwz: STRUCURE OF RAB6(GTP)-R6IP1 COMPLEX Solved by: X-RAY, Resolution: 3.20A, Identified by BLAST |
|
||||||||||||||||||||
|
2ffq: THE CRYSTAL STRUCTURE OF HUMAN NEURONAL RAB6B IN ITS ACTIVGTPGS-BOUND FORM Solved by: X-RAY, Resolution: 1.78A, Identified by BLAST |
|
||||||||||||||||||||
|
2fe4: THE CRYSTAL STRUCTURE OF HUMAN NEURONAL RAB6B IN ITS INACTIVE GDP-BOUND FORM Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST |
|
||||||||||||||||||||
|
4dkx: CRYSTAL STRUCTURE OF THE RAB 6A'(Q72L) Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST |
|
||||||||||||||||||||
|
2e9s: HUMAN NEURONAL RAB6B IN THREE INTERMEDIATE FORMS Solved by: X-RAY, Resolution: 1.78A, Identified by BLAST |
|
||||||||||||||||||||
|
1d5c: CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM RAB6 COMPLEXED WITH GDP Solved by: X-RAY, Resolution: 2.30A, 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.