Crystal structure of human heparanase, in complex with glucuronic acid configured aziridine probe JJB355

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).

Ligands and binding sites

• 6S6 · (1~{S},2~{R},3~{S},4~{S},5~{S},6~{R})-2-(8-azidooctylamino)-3,4,5,6-tetrakis(oxidanyl) cyclohexane-1-carboxylic acid · ligand · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · chains A, B
• EDO · 1,2-ethanediol · additive · 3 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, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 4286 Ų buried · 65 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan, 1 covalent, 1 disulfide (N-glycosylation, covalent ligand, disulfide).

Compared structures

• 5L9Y · Crystal structure of human heparanase, in complex with glucuronic acid configured… · 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 5L9Y · PDBe 5L9Y · UniProt Q9Y251