MolNFT v1 · #191167 · protein
Structure of human REP15:RAB3B complex.
8A4C · RAB15 effector protein: “Structure of human REP15:RAB3B complex.”. X-ray diffraction, 2 ligands (GNP, MG), 10 pockets (best druggability 0.70). MolNFT v1 #191167 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8A4C
- Type
- protein
- Length
- 744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAB15 effector protein; RAS-related protein rab-3B
- UniProt
- Q6BDI9, P20337
- Ligands
- GNP, MG
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAB15 effector protein | protein | 205 | 42% helix, 20% strand | Q6BDI9 |
| B, D | RAS-related protein rab-3B | protein | 170 | 35% helix, 27% strand | P20337 |
| C | RAB15 effector protein | protein | 199 | 38% helix, 21% strand | Q6BDI9 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.70 | 0.80 | 67 | GNP, MG |
| 2 | 388 | 0.67 | 0.80 | 47 | GNP, MG |
| 3 | 111 | 0.56 | 0.84 | 26 | empty |
| 4 | 135 | 0.50 | 0.79 | 22 | empty |
| 5 | 78 | 0.49 | 0.83 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1082 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 882 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 853 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 100 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 8A4C · Structure of human Rep15:Rab3B complex. · the same entry in another collection · chain A against A, TM-score 1.00
- P20337 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-3B (P20337) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q6BDI9 · AlphaFold monomer V2.0 prediction for RAB15 effector protein (Q6BDI9) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 Q6BDI9
- Every structure of UniProt P20337
- Elsewhere: RCSB PDB 8A4C · PDBe 8A4C · UniProt Q6BDI9 · UniProt P20337
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