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Crystal structure analysis of PIP4K2A

Analyse Crystal structure analysis of PIP4K2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UX9
Type: protein
Length: 628 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: UHJ
Pockets: 10 · best druggability 0.68

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	316	35% helix, 24% strand	P48426
B	Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (EC 2.7.1.149)	protein	312	34% helix, 24% strand	P48426

Ligands and binding sites

UHJ · N-[4-(5-{(Z)-[(2E)-2-imino-4-oxo-1,3-thiazolidin-5-ylidene]methyl}pyridin-3-yl)phenyl]methanesulfonamide · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	431	0.68	0.80	44	UHJ
2	429	0.67	0.79	53	UHJ
3	50	0.59	0.92	14	empty
4	54	0.42	0.82	12	empty
5	102	0.42	0.77	23	empty

Interfaces

1 interface between chains.

A–B · 1531 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

6UX9 · Crystal Structure Analysis of PIP4K2A · 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 6UX9 · PDBe 6UX9 · UniProt P48426

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