X-ray structure of phenylpyruvate decarboxylase in complex with 2-(1- hydroxyethyl)-3-deaza-thdp

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).

Ligands and binding sites

• S1T · 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1S)-1-hydroxyethyl]-3-methyl-2-thienyl}ethyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
• R1T · 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1-hydroxyethyl]-3-methyl-2-thienyl}ethyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3138 Ų buried · 33 hydrogen bonds · protein-protein

Compared structures

• 2Q5L · X-ray structure of phenylpyruvate decarboxylase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• P51852 · AlphaFold monomer V2.0 prediction for indole-3-pyruvate decarboxylase (P51852) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P51852
• Elsewhere: RCSB PDB 2Q5L · PDBe 2Q5L · UniProt P51852