MolNFT v1 · #114930 · protein
Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta with the inhibitor BQR695 in complex with GDP loaded RAB11
5C4G · RAS-related protein rab-11A: “Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta with the inhibitor…”. X-ray diffraction, 4 ligands (GDP, BQR, MG), 6 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 5C4G
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-11A; Phosphatidylinositol 4-kinase beta
- EC
- 2.7.1.67
- UniProt
- P62491, Q9UBF8
- Ligands
- GDP, BQR, MG, SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RAS-related protein rab-11A | protein | 156 | 33% helix, 26% strand | P62491 |
| E | Phosphatidylinositol 4-kinase beta (EC 2.7.1.67) | protein | 466 | 52% helix, 9% strand | Q9UBF8 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains B, E
- BQR · N~2~-[7-(3,4-dimethoxyphenyl)quinoxalin-2-yl]-N-methylglycinamide · ligand · chains E
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.68 | 0.77 | 53 | BQR |
| 2 | 354 | 0.65 | 0.79 | 32 | empty |
| 3 | 131 | 0.63 | 0.87 | 29 | empty |
| 4 | 164 | 0.59 | 0.82 | 24 | empty |
| 5 | 237 | 0.58 | 0.79 | 46 | MG, GDP |
Interfaces
1 interface between chains.
- B–E · 546 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5C4G · Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta… · the same entry in another collection · chain B against B, 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 0.98
- P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P62491
- Every structure of UniProt Q9UBF8
- Elsewhere: RCSB PDB 5C4G · PDBe 5C4G · UniProt P62491 · UniProt Q9UBF8
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