Research workbench
Crystal structure of GDP-bound RAB8:RABIN8
Analyse Crystal structure of GDP-bound RAB8:RABIN8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LHY
- Type
- protein
- Length
- 645 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-8A; Rab-3A-interacting protein
- UniProt
- P61006, Q96QF0
- Ligands
- GDP, SO4
- Pockets
- 5 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related protein rab-8A | protein | 175 | 39% helix, 27% strand | P61006 |
| C | Rab-3A-interacting protein | protein | 72 | 89% helix, 0% strand | Q96QF0 |
| D | Rab-3A-interacting protein | protein | 71 | 86% helix, 0% strand | Q96QF0 |
| E, F | Rab-3A-interacting protein | protein | 76 | 96% helix, 0% strand | Q96QF0 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.42 | 0.81 | 15 | empty |
| 2 | 122 | 0.42 | 0.76 | 20 | empty |
| 3 | 76 | 0.41 | 0.79 | 18 | empty |
| 4 | 105 | 0.36 | 0.74 | 15 | SO4 |
| 5 | 50 | 0.31 | 0.77 | 13 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1244 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 1020 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 793 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 730 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 540 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4LHY · Crystal structure of GDP-bound Rab8:Rabin8 · the same entry in another collection · chain F against F, TM-score 1.00
- P61006 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-8A (P61006) · a predicted model of the same protein · chain A against A, TM-score 0.92
- Q96QF0 · AlphaFold monomer V2.0 prediction for rab-3A-interacting protein (Q96QF0) · a predicted model of the same protein · chain C against A, TM-score 0.74
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 P61006
- Every structure of UniProt Q96QF0
- Elsewhere: RCSB PDB 4LHY · PDBe 4LHY · UniProt P61006 · UniProt Q96QF0
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