Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted glucuronic acid configured aziridine probe JJB355

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).

Ligands and binding sites

• GUX · (1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(azanylidene-{4}-azanylidene)amino]octyl]-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid · ligand · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
• CL · Chloride ion · ion · 3 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 7 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 4261 Ų buried · 66 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

• 5L9Z · Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9Y251 · AlphaFold monomer V2.0 prediction for heparanase (Q9Y251) · 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 Q9Y251
• Elsewhere: RCSB PDB 5L9Z · PDBe 5L9Z · UniProt Q9Y251