MolNFT v1 · #147517 · protein

Pyruvate decarboxylase from kluyveromyces lactis

6EFG: “Pyruvate decarboxylase from kluyveromyces lactis”. X-ray diffraction, 2 ligands (TPP, MG), 19 pockets (best druggability 0.77). MolNFT v1 #147517 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6EFG
Type: protein
Length: 2,143 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate decarboxylase
EC: 4.1.1.1
UniProt: Q12629
Ligands: TPP, MG
Pockets: 19 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyruvate decarboxylase (EC 4.1.1.1)	protein	536	40% helix, 18% strand	Q12629
B	Pyruvate decarboxylase (EC 4.1.1.1)	protein	532	42% helix, 18% strand	Q12629
D	Pyruvate decarboxylase (EC 4.1.1.1)	protein	537	42% helix, 18% strand	Q12629
E	Pyruvate decarboxylase (EC 4.1.1.1)	protein	538	41% helix, 18% strand	Q12629

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, D, E
MG · Magnesium ion · metal · 4 copies · chains A, B, D, E

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

Pockets

19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	758	0.77	0.81	97	empty
2	883	0.76	0.79	102	TPP, MG
3	908	0.75	0.79	110	TPP, MG
4	533	0.73	0.81	52	empty
5	782	0.73	0.78	84	TPP, MG

Interfaces

6 interfaces between chains.

D–E · 2883 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2856 Å² buried · 45 hydrogen bonds · protein-protein
A–E · 666 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 370 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 147 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6EFG · Pyruvate decarboxylase from Kluyveromyces lactis · the same entry in another collection · chain E against E, TM-score 1.00
Q12629 · AlphaFold monomer V2.0 prediction for pyruvate decarboxylase (Q12629) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 Q12629
Elsewhere: RCSB PDB 6EFG · PDBe 6EFG · UniProt Q12629

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