Crystallization of a 45 kda peroxygenase- peroxidase from the mushroom agrocybe aegerita and structure determination by sad utilizing only the haem iron

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 6% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
• MZ0 · 1H-imidazol-5-ylmethanol · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 6 copies · chains B, A
• MG · Magnesium ion · metal · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 6 copies · chains A, B
• CL · Chloride ion · ion · 4 copies · chains A, B
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1301 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

• 2YOR · Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita… · the same entry in another collection · chain A against A, TM-score 1.00
• B9W4V6 · AlphaFold monomer V2.0 prediction for aromatic peroxygenase (B9W4V6) · 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 B9W4V6
• Elsewhere: RCSB PDB 2YOR · PDBe 2YOR · UniProt B9W4V6