MolNFT v1 · #37871 · protein
Crystal structure of human RAB3D in complex with GDP
2GF9 · RAS-related protein rab-3D: “Crystal structure of human RAB3D in complex with GDP”. X-ray diffraction, 3 ligands (GDP, MG, UNX), 1 pocket (best druggability 0.52). MolNFT v1 #37871 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2GF9
- Type
- protein
- Length
- 176 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-3D
- UniProt
- O95716
- Ligands
- GDP, MG, UNX
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-3D | protein | 176 | 35% helix, 26% strand | O95716 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- UNX · Unknown atom or ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.52 | 0.76 | 33 | MG, GDP |
Compared structures
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 O95716
- Elsewhere: RCSB PDB 2GF9 · PDBe 2GF9 · UniProt O95716
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