MolNFT v1 · #28279 · protein

Pyruvate oxidase variant V265A from lactobacillus plantarum

1Y9D: “Pyruvate oxidase variant V265A from lactobacillus plantarum”. X-ray diffraction, 5 ligands (TPP, FAD, MG), 20 pockets (best druggability 0.82). MolNFT v1 #28279 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1Y9D
Type: protein
Length: 2,246 residues
Chains: 4
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, SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate oxidase (EC 1.2.3.3)	protein	558	44% helix, 18% strand	P37063
B	Pyruvate oxidase (EC 1.2.3.3)	protein	572	43% helix, 17% strand	P37063
C	Pyruvate oxidase (EC 1.2.3.3)	protein	556	43% helix, 18% strand	P37063
D	Pyruvate oxidase (EC 1.2.3.3)	protein	560	43% helix, 18% strand	P37063

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 4 copies · chains A, C, B, D
FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 2 copies · chains A, C, B, D
SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	896	0.82	0.84	100	MG, TPP, FAD, SO4
2	732	0.80	0.84	97	MG, TPP, FAD, SO4
3	711	0.80	0.84	91	SO4, MG, TPP, FAD
4	260	0.77	0.90	56	SO4, MG, TPP
5	189	0.76	0.92	37	empty

Interfaces

6 interfaces between chains.

B–D · 2946 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 2882 Å² buried · 50 hydrogen bonds · protein-protein
A–B · 830 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 487 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 407 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1Y9D · Pyruvate Oxidase variant V265A from Lactobacillus plantarum · the same entry in another collection · chain D against D, 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 1Y9D · PDBe 1Y9D · UniProt P37063

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