Research workbench
The crystal structure of human neuronal RAB6B in its inactive GDP-bound form
Analyse The crystal structure of human neuronal RAB6B in its inactive GDP-bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FE4
- Type
- protein
- Length
- 163 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-6B
- EC
- 3.6.1.-
- UniProt
- Q9NRW1
- Ligands
- GDP, MG, NO3
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-6B (EC 3.6.1.-) | protein | 163 | 35% helix, 25% strand | Q9NRW1 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NO3 · Nitrate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.54 | 0.78 | 32 | MG, NO3, GDP |
| 2 | 53 | 0.33 | 0.78 | 16 | empty |
Compared structures
- 2FE4 · The crystal structure of human neuronal Rab6B in its inactive GDP-bound form · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NRW1 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-6B (Q9NRW1) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9NRW1
- Elsewhere: RCSB PDB 2FE4 · PDBe 2FE4 · UniProt Q9NRW1
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