F448H mutant of tyrosine phenol-lyase from citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosine

Structure

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

Ligands and binding sites

• P61 · (2E)-3-(3-fluoro-4-hydroxyphenyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}propanoic acid · ligand · 4 copies · chains A, B, C, D
• K · Potassium ion · metal · 4 copies · chains A, B, C, D
• PGE · Triethylene glycol · additive · 13 copies · chains A, D, B, C
• PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, D, C
• P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 2 copies · chains B, C, A, D
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
• EDO · 1,2-ethanediol · additive · chains B
• 1PE · Pentaethylene glycol · additive · chains B, C

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

Pockets

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

Interfaces

6 interfaces between chains.

• C–D · 2392 Ų buried · 36 hydrogen bonds · protein-protein
• A–B · 2339 Ų buried · 39 hydrogen bonds · protein-protein
• B–C · 1626 Ų buried · 30 hydrogen bonds · protein-protein
• A–D · 1605 Ų buried · 31 hydrogen bonds · protein-protein
• A–C · 429 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 2YCP · F448H mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid… · the same entry in another collection · chain D against D, 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 2YCP · PDBe 2YCP · UniProt P31013