M379A mutant tyrosine phenol-lyase complexed with L-methionine

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).

Ligands and binding sites

• PN9 · (4Z)-4-({[(1E)-1-carboxy-3-(methylsulfanyl) propylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate · ligand · 3 copies · chains A, D, B, C
• PLP · Pyridoxal-5'-phosphate · ligand · chains A, D
• K · Potassium ion · metal · 4 copies · chains A, D, B, C
• CS · Cesium ion · metal · 3 copies · chains A, C, D
• DMS · Dimethyl sulfoxide · additive · 7 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–C · 2389 Ų buried · 38 hydrogen bonds · protein-protein
• A–D · 2378 Ų buried · 38 hydrogen bonds · protein-protein
• B–D · 1706 Ų buried · 36 hydrogen bonds · protein-protein
• A–C · 1627 Ų buried · 34 hydrogen bonds · protein-protein
• A–B · 413 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 7TCS · M379A mutant tyrosine phenol-lyase complexed with L-methionine · the same entry in another collection · chain A against A, 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 7TCS · PDBe 7TCS · UniProt P31013