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Crystal structure of the reaction intermediate between pyruvate oxidase containing FAD and tpp, and substrate pyruvate

Analyse Crystal structure of the reaction intermediate between pyruvate oxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1V5G
Type: protein
Length: 589 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate oxidase
EC: 1.2.3.3
Ligands: FAD, HTL, MG
Pockets: 4 · best druggability 0.71

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate oxidase (EC 1.2.3.3)	protein	589	42% helix, 16% strand	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
HTL · 2-acetyl-thiamine diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	717	0.71	0.78	54	FAD
2	146	0.61	0.84	26	empty
3	58	0.54	0.88	19	empty
4	79	0.54	0.86	17	MG, HTL

Compared structures

1V5G · Crystal Structure of the Reaction Intermediate between Pyruvate oxidase containing FAD… · the same entry in another collection · 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
Elsewhere: RCSB PDB 1V5G · PDBe 1V5G

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