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Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from escherichia COLI

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PDB: 3EYA
Type: protein
Length: 6,268 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate dehydrogenase [cytochrome]
EC: 1.2.2.2
UniProt: P07003
Ligands: TPP, FAD, MG, PO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 10 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	527	43% helix, 18% strand	P07003
B	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	524	43% helix, 18% strand	P07003
C	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	522	43% helix, 18% strand	P07003
D	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	520	43% helix, 18% strand	P07003
E, H	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	522	43% helix, 18% strand	P07003
F	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	521	43% helix, 18% strand	P07003
G	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	519	43% helix, 18% strand	P07003
I, L	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	523	43% helix, 18% strand	P07003
J	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	522	43% helix, 18% strand	P07003
K	Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2)	protein	523	43% helix, 18% strand	P07003

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
FAD · Flavin-adenine dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
PO4 · Phosphate ion · ion · 36 copies · chains A, D, B, C, E, F, G, H, I, J, K, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1150	0.88	0.90	166	PO4, TPP, FAD, MG
2	631	0.85	0.90	89	FAD
3	505	0.84	0.91	84	PO4, TPP, FAD
4	742	0.84	0.87	64	empty
5	369	0.83	0.92	67	PO4, TPP, FAD, MG

Interfaces

23 interfaces between chains.

A–B · 2801 Å² buried · 37 hydrogen bonds · protein-protein
K–L · 2733 Å² buried · 36 hydrogen bonds · protein-protein
I–J · 2706 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2661 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 2631 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

3EYA · Structural basis for membrane binding and catalytic activation of the peripheral membrane… · the same entry in another collection · chain L against L, 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 P07003
Elsewhere: RCSB PDB 3EYA · PDBe 3EYA · UniProt P07003

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