Crystal structure of human myeloperoxidase isoform C crystallized in space group P2(1) at pH 5.5 and 20 deg C

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 9% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C, B, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, D, B, A
• MAN · alpha-D-mannopyranose · sugar · 4 copies · chains D, B, C, A
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains D, C
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C, D
• CA · Calcium ion · metal · 2 copies · chains A, C, B, D
• CL · Chloride ion · ion · 2 copies · chains A, C, B, D

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–C · 5746 Ų buried · 109 hydrogen bonds · protein-protein
• B–D · 5709 Ų buried · 105 hydrogen bonds · protein-protein
• A–B · 615 Ų buried · 4 hydrogen bonds · protein-protein
• C–D · 377 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 264 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 6 cofactor, 6 glycan (disulfide, heme attachment, N-glycosylation).

Compared structures

• 1MHL · Crystal structure of human myeloperoxidase isoform C crystallized in space group P2(1) at… · the same entry in another collection · chain A against A, TM-score 1.00
• P05164 · AlphaFold monomer V2.0 prediction for myeloperoxidase (P05164) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P05164
• Elsewhere: RCSB PDB 1MHL · PDBe 1MHL · UniProt P05164