Research workbench
Crystal structure of mouse RAB27B bound to GDP in monoclinic space group
Analyse Crystal structure of mouse RAB27B bound to GDP in monoclinic space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IF0
- Type
- protein
- Length
- 349 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, MG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-27B (EC 3.6.5.2) | protein | 174 | 37% helix, 30% strand | Q99P58 |
| B | RAS-related protein rab-27B (EC 3.6.5.2) | protein | 175 | 36% helix, 30% strand | Q99P58 |
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 | 285 | 0.58 | 0.77 | 32 | MG |
| 2 | 217 | 0.53 | 0.77 | 29 | MG |
| 3 | 119 | 0.39 | 0.74 | 19 | empty |
| 4 | 125 | 0.38 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3327 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2IF0 · Crystal Structure of mouse Rab27b bound to GDP in monoclinic 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 0.71
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 2IF0 · PDBe 2IF0 · UniProt Q99P58
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