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Crystal structure of pyruvate oxidase complexed with FAD and tpp, from aerococcus viridans

Analyse Crystal structure of pyruvate oxidase complexed with FAD and tpp, from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1V5F
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, TPP, MG, SO4
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate oxidase (EC 1.2.3.3)	protein	589	41% helix, 16% strand	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
TPP · Thiamine diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
SO4 · Sulfate ion · ion · 4 copies · chains A

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

Pockets

5 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	796	0.74	0.79	64	FAD
2	140	0.60	0.84	27	empty
3	74	0.57	0.88	18	empty
4	90	0.50	0.83	18	MG, TPP
5	79	0.37	0.77	15	empty

Compared structures

1V5F · Crystal Structure of Pyruvate oxidase complexed with FAD and TPP, from Aerococcus viridans · 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 1V5F · PDBe 1V5F

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