MolNFT v1 · #36506 · protein
The crystal structure of human RAB27B bound to GDP
2F7S · RAS-related protein rab-27B: “The crystal structure of human RAB27B bound to GDP”. X-ray diffraction, 2 ligands (GDP, MG), 4 pockets (best druggability 0.58). MolNFT v1 #36506 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2F7S
- Type
- protein
- Length
- 355 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-27B
- UniProt
- O00194
- Ligands
- GDP, MG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-27B | protein | 179 | 36% helix, 32% strand | O00194 |
| B | RAS-related protein rab-27B | protein | 176 | 32% helix, 31% strand | O00194 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.58 | 0.77 | 27 | empty |
| 2 | 241 | 0.53 | 0.76 | 26 | empty |
| 3 | 80 | 0.35 | 0.75 | 17 | empty |
| 4 | 61 | 0.29 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3331 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 O00194
- Elsewhere: RCSB PDB 2F7S · PDBe 2F7S · UniProt O00194
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