MolNFT v1 · #56422 · protein
Crystal structure of the small GTPase RAB27B complexed with the slp homology domain of SLAC2-A/MELANOPHILIN
2ZET · RAS-related protein rab-27B: “Crystal structure of the small GTPase RAB27B complexed with the slp homology domain of SLAC2-A/MELANOPHILIN”. X-ray diffraction, 4 ligands (GTP, ZN, MG), 9 pockets (best druggability 0.59). MolNFT v1…
- PDB
- 2ZET
- Type
- protein
- Length
- 637 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-27B; Melanophilin
- UniProt
- Q99P58, Q91V27
- Ligands
- GTP, ZN, MG, SO4
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-27B | protein | 181 | 36% helix, 27% strand | Q99P58 |
| C, D | Melanophilin | protein | 141 | 57% helix, 7% strand | Q91V27 |
| B | RAS-related protein rab-27B | protein | 174 | 37% helix, 24% strand | Q99P58 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.59 | 0.77 | 33 | empty |
| 2 | 232 | 0.57 | 0.79 | 34 | MG, GTP |
| 3 | 184 | 0.54 | 0.79 | 34 | MG, GTP |
| 4 | 82 | 0.51 | 0.84 | 15 | empty |
| 5 | 92 | 0.43 | 0.79 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1928 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1780 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 353 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2ZET · Crystal structure of the small GTPase Rab27B complexed with the Slp homology domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q99P58 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-27B (Q99P58) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q91V27 · AlphaFold monomer V2.0 prediction for melanophilin (Q91V27) · a predicted model of the same protein · chain C 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 Q99P58
- Every structure of UniProt Q91V27
- Elsewhere: RCSB PDB 2ZET · PDBe 2ZET · UniProt Q99P58 · UniProt Q91V27
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