Structural insights into the pre-reaction state of pyruvate decarboxylase from zymomonas mobilis

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).

Ligands and binding sites

• TPU · 2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl trihydrogen diphosphate · ligand · 8 copies · chains A, B, E, F, V, Z, X, Y
• PYR · Pyruvic acid · ligand · 3 copies · chains E, F, V, Z
• MG · Magnesium ion · metal · 8 copies · chains A, B, E, F, V, X, Y, Z

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.

Interfaces

15 interfaces between chains.

• A–B · 4283 Ų buried · 79 hydrogen bonds · protein-protein
• V–Z · 4279 Ų buried · 78 hydrogen bonds · protein-protein
• X–Y · 4273 Ų buried · 79 hydrogen bonds · protein-protein
• E–F · 4265 Ų buried · 76 hydrogen bonds · protein-protein
• B–E · 1220 Ų buried · 30 hydrogen bonds · protein-protein

Compared structures

• 2WVA · Structural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas… · the same entry in another collection · chain Z against Z, 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 2WVA · PDBe 2WVA · UniProt P06672