Research workbench
Crystal structure of the phosphatidylinositol 4-kinase IIbeta
Analyse Crystal structure of the phosphatidylinositol 4-kinase IIbeta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WTV
- Type
- protein
- Length
- 873 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Enterobacteria phage T4; Homo sapiens
- Molecule
- Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type…
- EC
- 2.7.1.67, 3.2.1.17
- UniProt
- Q8TCG2, P00720
- Ligands
- ATP
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta (EC 2.7.1.67, 3.2.1.17) | protein | 447 | 50% helix, 12% strand | Q8TCG2, P00720 |
| B | Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta (EC 2.7.1.67, 3.2.1.17) | protein | 426 | 52% helix, 10% strand | Q8TCG2, P00720 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.80 | 0.81 | 112 | ATP |
| 2 | 316 | 0.64 | 0.80 | 52 | ATP |
| 3 | 289 | 0.58 | 0.77 | 23 | empty |
| 4 | 218 | 0.54 | 0.77 | 24 | empty |
| 5 | 133 | 0.47 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1291 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4WTV · Crystal structure of the phosphatidylinositol 4-kinase iibeta · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TCG2 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-kinase type 2-beta (Q8TCG2) · a predicted model of the same protein · chain B against A, TM-score 0.68
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 Q8TCG2
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 4WTV · PDBe 4WTV · UniProt Q8TCG2 · UniProt P00720
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