Crystal structure of the complex of bovine lactoperoxidase with 4- allyl-2-methoxyphenol at 2.6 a resolution

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 9% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · chains A
• EUG · 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
• CA · Calcium ion · metal · chains A
• IOD · Iodide ion · ion · 10 copies · chains A
• SCN · Thiocyanate ion · ion · chains A
• EDO · 1,2-ethanediol · additive · 2 copies · chains A
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
• GOL · Glycerol · additive · chains A

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).

Compared structures

• 3R5O · Crystal structure of the complex of bovine lactoperoxidase with 4-allyl-2-methoxyphenol… · the same entry in another collection · chain A against A, TM-score 1.00
• P80025 · AlphaFold monomer V2.0 prediction for lactoperoxidase (P80025) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P80025
• Elsewhere: RCSB PDB 3R5O · PDBe 3R5O · UniProt P80025