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Crystal structure of human phosphatidylinositol 4-kinase III beta (PI4KIIIBETA) in complex with ligand 44
Analyse Crystal structure of human phosphatidylinositol 4-kinase III beta (PI4KIIIBETA)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GL3
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4-kinase BETA,PHOSPHATIDYLINOSITOL 4- kinase beta
- EC
- 2.7.1.67
- UniProt
- Q9UBF8
- Ligands
- EMW
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4-kinase BETA,PHOSPHATIDYLINOSITOL 4- kinase beta (EC 2.7.1.67) | protein | 354 | 46% helix, 13% strand | Q9UBF8 |
| B | Phosphatidylinositol 4-kinase BETA,PHOSPHATIDYLINOSITOL 4- kinase beta (EC 2.7.1.67) | protein | 301 | 47% helix, 13% strand | Q9UBF8 |
Ligands and binding sites
- EMW · (3~{S})-4-(6-azanyl-1-methyl-pyrazolo[3,4-d]pyrimidin-4-yl)-~{N}-(4-methoxy-2-methyl-phenyl)-3-methyl-piperazine-1-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.75 | 0.86 | 37 | empty |
| 2 | 574 | 0.72 | 0.80 | 52 | EMW |
| 3 | 396 | 0.60 | 0.75 | 36 | empty |
| 4 | 125 | 0.50 | 0.79 | 22 | empty |
| 5 | 81 | 0.44 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1295 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6GL3 · Crystal structure of human Phosphatidylinositol 4-kinase III beta (PI4KIIIbeta) in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBF8 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-kinase beta (Q9UBF8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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
- Elsewhere: RCSB PDB 6GL3 · PDBe 6GL3 · UniProt Q9UBF8
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