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Crystal structure of human RAB5B in complex with GDP
Analyse Crystal structure of human RAB5B in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HEI
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-5B
- UniProt
- P61020
- Ligands
- GDP, D1D
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-5B | protein | 163 | 38% helix, 23% strand | P61020 |
| B | RAS-related protein rab-5B | protein | 165 | 38% helix, 25% strand | P61020 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- D1D · (4S,5S)-1,2-dithiane-4,5-diol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.55 | 0.81 | 27 | GDP |
| 2 | 142 | 0.52 | 0.80 | 26 | GDP |
Interfaces
1 interface between chains.
- A–B · 726 Ų buried · 13 hydrogen bonds · protein-protein
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 P61020
- Elsewhere: RCSB PDB 2HEI · PDBe 2HEI · UniProt P61020
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