Tyrosine phenol-lyase from citrobacter freundii in complex with pyridine N-oxide and the quinonoid intermediate formed with L-alanine

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).

Ligands and binding sites

• 9PO · Pyridine-N-oxide · ligand · 3 copies · chains A, B
• PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
• PLI · (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}propanoic acid · ligand · chains A, B
• K · Potassium ion · metal · 2 copies · chains A, B
• PO4 · Phosphate ion · ion · chains A
• P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains B

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2348 Ų buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).

Compared structures

• 2YCT · Tyrosine phenol-lyase from Citrobacter freundii in complex with pyridine N-oxide and the… · the same entry in another collection · chain B against B, TM-score 1.00
• P31013 · AlphaFold monomer V2.0 prediction for tyrosine phenol-lyase (P31013) · 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 P31013
• Elsewhere: RCSB PDB 2YCT · PDBe 2YCT · UniProt P31013