Research workbench
Crystal structure of human phosphatidylinositol-5-phosphate 4-kinase type-2 alpha
Analyse Crystal structure of human phosphatidylinositol-5-phosphate 4-kinase type-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YBX
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha
- EC
- 2.7.1.149
- UniProt
- P48426
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha (EC 2.7.1.149) | protein | 322 | 36% helix, 23% strand | P48426 |
| B | Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha (EC 2.7.1.149) | protein | 312 | 35% helix, 24% strand | P48426 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.75 | 0.96 | 30 | empty |
| 2 | 481 | 0.68 | 0.79 | 57 | empty |
| 3 | 362 | 0.67 | 0.80 | 42 | empty |
| 4 | 119 | 0.44 | 0.77 | 21 | empty |
| 5 | 101 | 0.41 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1485 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2YBX · Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha · the same entry in another collection · chain A against A, TM-score 1.00
- P48426 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 5-phosphate 4-kinase type-2… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P48426
- Elsewhere: RCSB PDB 2YBX · PDBe 2YBX · UniProt P48426
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