Research workbench
Structure of the extremely slow GTPase RAB6A in the GTP bound form at 1.8 resolution
Analyse Structure of the extremely slow GTPase RAB6A in the GTP bound form at 1.8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GIL
- Type
- protein
- Length
- 645 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-6A
- UniProt
- P20340
- Ligands
- GTP, MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | RAS-related protein rab-6A | protein | 161 | 36% helix, 25% strand | P20340 |
| B | RAS-related protein rab-6A | protein | 162 | 40% helix, 27% strand | P20340 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.74 | 0.82 | 57 | MG, GTP |
| 2 | 578 | 0.73 | 0.81 | 73 | MG, GTP |
| 3 | 336 | 0.71 | 0.84 | 42 | MG, GTP |
| 4 | 526 | 0.69 | 0.79 | 64 | MG, GTP |
| 5 | 50 | 0.40 | 0.81 | 13 | empty |
Interfaces
3 interfaces between chains.
- C–D · 729 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 666 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 419 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2GIL · Structure of the extremely slow GTPase Rab6A in the GTP bound form at 1.8 resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P20340 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-6A (P20340) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P20340
- Elsewhere: RCSB PDB 2GIL · PDBe 2GIL · UniProt P20340
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