MolNFT v1 · #55061 · protein
Crystal structure of D. melanogaster RAB6 GTPase bound to gmppnp
2Y8E · Rab-protein 6: “Crystal structure of D. melanogaster RAB6 GTPase bound to gmppnp”. X-ray diffraction, 3 ligands (GNP, MG, SO4), 3 pockets (best druggability 0.70). MolNFT v1 #55061 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2Y8E
- Type
- protein
- Length
- 332 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rab-protein 6
- UniProt
- O18334
- Ligands
- GNP, MG, SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rab-protein 6 | protein | 165 | 39% helix, 30% strand | O18334 |
| B | Rab-protein 6 | protein | 167 | 40% helix, 28% strand | O18334 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.70 | 0.81 | 49 | GNP, MG |
| 2 | 329 | 0.67 | 0.82 | 46 | GNP, MG |
| 3 | 65 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 710 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2Y8E · Crystal structure of D. melanogaster Rab6 GTPase bound to GMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
- O18334 · AlphaFold monomer V2.0 prediction for RAS-related protein RAB6 (O18334) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O18334
- Elsewhere: RCSB PDB 2Y8E · PDBe 2Y8E · UniProt O18334
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