MolNFT v1 · #114920 · protein
Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in complex with GTP gamma S loaded RAB11
5C46 · Phosphatidylinositol 4-kinase beta: “Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in complex with GTP…”. X-ray diffraction, 3 ligands (GSP, MG, SO4), 8 pockets (best druggability 0.72).…
- PDB
- 5C46
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4-kinase beta; RAS-related protein rab-11A
- EC
- 2.7.1.67
- UniProt
- Q9UBF8, P62491
- Ligands
- GSP, MG, SO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) | protein | 469 | 53% helix, 9% strand | Q9UBF8 |
| F | RAS-related protein rab-11A | protein | 175 | 36% helix, 28% strand | P62491 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · chains E, F
- MG · Magnesium ion · metal · chains F
- SO4 · Sulfate ion · ion · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.72 | 0.78 | 63 | empty |
| 2 | 339 | 0.68 | 0.82 | 46 | GSP, MG |
| 3 | 416 | 0.65 | 0.79 | 42 | empty |
| 4 | 85 | 0.47 | 0.81 | 16 | empty |
| 5 | 110 | 0.42 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- E–F · 620 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5C46 · Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9UBF8 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-kinase beta (Q9UBF8) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 Q9UBF8
- Every structure of UniProt P62491
- Elsewhere: RCSB PDB 5C46 · PDBe 5C46 · UniProt Q9UBF8 · UniProt P62491
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