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Crystal structure of human pyridoxal phosphate phosphatase

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

PDB: 2OYC
Type: protein
Length: 292 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal phosphate phosphatase
EC: 3.1.3.74
UniProt: Q96GD0
Ligands: NA, WO4
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxal phosphate phosphatase (EC 3.1.3.74)	protein	292	41% helix, 20% strand	Q96GD0

Ligands and binding sites

NA · Sodium ion · metal · chains A
WO4 · Tungstate(vi)ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	242	0.65	0.83	33	WO4
2	55	0.29	0.74	15	empty

Modifications

Observed in the structure: 3 modified (engineered).

Compared structures

2OYC · Crystal structure of human pyridoxal phosphate phosphatase · the same entry in another collection · chain A against A, TM-score 1.00
Q96GD0 · AlphaFold monomer V2.0 prediction for pyridoxal phosphate phosphatase (Q96GD0) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q96GD0
Elsewhere: RCSB PDB 2OYC · PDBe 2OYC · UniProt Q96GD0

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