MolNFT v1 · #163517 · protein
Structure of the human RAB39B in complex with gmppnp
6S5F · RAS-related protein rab-39B: “Structure of the human RAB39B in complex with gmppnp”. X-ray diffraction, 2 ligands (GNP, MG), 2 pockets (best druggability 0.46). MolNFT v1 #163517 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6S5F
- Type
- protein
- Length
- 189 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-39B
- UniProt
- Q96DA2
- Ligands
- GNP, MG
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-39B | protein | 189 | 32% helix, 28% strand | Q96DA2 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.46 | 0.78 | 24 | GNP, MG |
| 2 | 87 | 0.45 | 0.80 | 22 | empty |
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 Q96DA2
- Elsewhere: RCSB PDB 6S5F · PDBe 6S5F · UniProt Q96DA2
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