MolNFT v1 · #36220 · protein

Pyruvate oxidase variant F479W

2EZ4: “Pyruvate oxidase variant F479W”. X-ray diffraction, 5 ligands (TPP, FAD, MG), 13 pockets (best druggability 0.78). MolNFT v1 #36220 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2EZ4
Type: protein
Length: 1,170 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate oxidase
EC: 1.2.3.3
UniProt: P37063
Ligands: TPP, FAD, MG, NA, PO4
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pyruvate oxidase (EC 1.2.3.3)	protein	585	42% helix, 16% strand	P37063

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	507	0.78	0.85	60	FAD
2	378	0.75	0.85	55	FAD
3	106	0.68	0.91	29	TPP
4	100	0.66	0.90	29	MG, TPP
5	249	0.55	0.77	29	empty

Interfaces

1 interface between chains.

A–B · 1384 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

2EZ4 · Pyruvate oxidase variant F479W · the same entry in another collection · chain A against A, TM-score 1.00
P37063 · AlphaFold monomer V2.0 prediction for pyruvate oxidase (P37063) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P37063
Elsewhere: RCSB PDB 2EZ4 · PDBe 2EZ4 · UniProt P37063

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