Pyruvate decarboxylase from zymomonas mobilis

Structure

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

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.

Interfaces

6 interfaces between chains.

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