MolNFT v1 · #29979 · protein

Pyruvate decarboxylase from zymomonas mobilis

1ZPD: “Pyruvate decarboxylase from zymomonas mobilis”. X-ray diffraction, 2 ligands (DPX, MG), 20 pockets (best druggability 0.81). MolNFT v1 #29979 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZPD
Type: protein
Length: 2,260 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate decarboxylase
EC: 4.1.1.1
UniProt: P06672
Ligands: DPX, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F	Pyruvate decarboxylase (EC 4.1.1.1)	protein	565	41% helix, 18% strand	P06672

Ligands and binding sites

DPX · Mono-{4-[(4-amino-2-methyl-pyrimidin-5-ylmethyl)-amino]-2-hydroxy-3-mercapto-pent-3-enyl-phosphono} ester · ligand · 4 copies · chains A, B, E, F
MG · Magnesium ion · metal · 4 copies · chains A, B, E, F
CIT · Citric acid · additive · 4 copies · chains A, F, B, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.81	0.97	43	DPX
2	165	0.81	0.97	43	MG, DPX
3	168	0.81	0.97	45	DPX
4	157	0.81	0.97	45	DPX
5	125	0.75	0.94	40	empty

Interfaces

6 interfaces between chains.

E–F · 4361 Å² buried · 73 hydrogen bonds · protein-protein
A–B · 4347 Å² buried · 74 hydrogen bonds · protein-protein
A–F · 1356 Å² buried · 31 hydrogen bonds · protein-protein
B–E · 1348 Å² buried · 31 hydrogen bonds · protein-protein
A–E · 711 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1ZPD · Pyruvate decarboxylase from zymomonas mobilis · the same entry in another collection · chain A against A, TM-score 1.00
P06672 · AlphaFold monomer V2.0 prediction for pyruvate decarboxylase (P06672) · 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 P06672
Elsewhere: RCSB PDB 1ZPD · PDBe 1ZPD · UniProt P06672

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.