Research workbench
Crystal structure of the catalytic domain of selenomethionine substituted human PI4KIIALPHA in complex with ADP
Analyse Crystal structure of the catalytic domain of selenomethionine substituted human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HND
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4-kinase type 2-alpha
- EC
- 2.7.1.67
- UniProt
- Q9BTU6
- Ligands
- ADP
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4-kinase type 2-alpha (EC 2.7.1.67) | protein | 353 | 45% helix, 11% strand | Q9BTU6 |
| B | Phosphatidylinositol 4-kinase type 2-alpha (EC 2.7.1.67) | protein | 337 | 46% helix, 11% strand | Q9BTU6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.72 | 0.81 | 30 | empty |
| 2 | 345 | 0.65 | 0.80 | 44 | ADP |
| 3 | 344 | 0.62 | 0.78 | 50 | ADP |
| 4 | 260 | 0.59 | 0.79 | 31 | empty |
| 5 | 190 | 0.55 | 0.79 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4HND · Crystal structure of the catalytic domain of Selenomethionine substituted human… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BTU6 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4-kinase type 2-alpha (Q9BTU6) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q9BTU6
- Elsewhere: RCSB PDB 4HND · PDBe 4HND · UniProt Q9BTU6
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