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

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 25% 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
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · chains A
• EDO · 1,2-ethanediol · additive · 6 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 4 glycan, 2 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).

Compared structures

• 5LA7 · Crystal structure of human proheparanase, 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 5LA7 · PDBe 5LA7 · UniProt Q9Y251