MolNFT v1 · #40075 · protein
Crystal structure of mouse RAB27B bound to GDP in hexagonal space group
2IEY · RAS-related protein rab-27B: “Crystal structure of mouse RAB27B bound to GDP in hexagonal space group”. X-ray diffraction, 1 ligand (GDP), 2 pockets (best druggability 0.51). MolNFT v1 #40075 on GenesisL1: 3D structure, binding…
- PDB
- 2IEY
- Type
- protein
- Length
- 327 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-27B
- EC
- 3.6.5.2
- UniProt
- Q99P58
- Ligands
- GDP
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-27B (EC 3.6.5.2) | protein | 164 | 32% helix, 27% strand | Q99P58 |
| B | RAS-related protein rab-27B (EC 3.6.5.2) | protein | 163 | 26% helix, 31% strand | Q99P58 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.51 | 0.79 | 19 | empty |
| 2 | 87 | 0.45 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3375 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2IEY · Crystal Structure of mouse Rab27b bound to GDP in hexagonal space group · 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 0.78
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
- Elsewhere: RCSB PDB 2IEY · PDBe 2IEY · UniProt Q99P58
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