MolNFT v1 · #105944 · protein
Drosophila melanogaster RAB3 bound to gmppnp
4RKF · RAS-related protein rab-3: “Drosophila melanogaster RAB3 bound to gmppnp”. X-ray diffraction, 2 ligands (GNP, MG), 4 pockets (best druggability 0.59). MolNFT v1 #105944 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RKF
- Type
- protein
- Length
- 343 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-3
- UniProt
- P25228
- Ligands
- GNP, MG
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-3 | protein | 171 | 37% helix, 29% strand | P25228 |
| B | RAS-related protein rab-3 | protein | 172 | 37% helix, 28% strand | P25228 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.59 | 0.75 | 49 | empty |
| 2 | 147 | 0.54 | 0.81 | 28 | GNP, MG |
| 3 | 159 | 0.54 | 0.80 | 32 | GNP, MG |
| 4 | 65 | 0.38 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 543 Ų buried · 12 hydrogen bonds · protein-protein
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 P25228
- Elsewhere: RCSB PDB 4RKF · PDBe 4RKF · UniProt P25228
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