Mode of ligand binding and assignment of subsites in mammalian peroxidases: crystal structure of lactoperoxidase complexes with acetyl salycylic acid, salicylhydroxamic acid and benzylhydroxamic acid

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 9% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · chains A
• AIN · 2-(acetyloxy)benzoic acid · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• CA · Calcium ion · metal · chains A
• IOD · Iodide ion · ion · 8 copies · chains A
• SCN · Thiocyanate ion · ion · chains A

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

Pockets

9 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

• 3GCL · Mode of ligand binding and assignment of subsites in mammalian peroxidases: crystal… · 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 3GCL · PDBe 3GCL · UniProt P80025