› 8ohr

X-ray diffraction
1.8Å resolution

Crystal structure of human heparanase in complex with glucuronic acid configured 3-geminal diol iminosugar inhibitor

Released:
DOI: 10.2210/pdb8ohr/pdb
PDB entry 8ohr coloured by chain, front view.
PDB entry 8ohr coloured by chain, side view.
PDB entry 8ohr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular Basis for Inhibition of Heparanases and β-Glucuronidases by Siastatin B.
Chen Y, van den Nieuwendijk AMCH, Wu L, Moran E, Skoulikopoulou F, van Riet V, Overkleeft HS, Davies GJ, Armstrong Z
OpenAccess logo J Am Chem Soc (2023)
PMID: 38118176

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195099 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Heparanase 50 kDa subunit Chain: AAA
Molecule details ›
Chain: AAA
Length: 385 amino acids
Theoretical weight: 43.33 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
Heparanase 8 kDa subunit Chain: BBB
Molecule details ›
Chain: BBB
Length: 74 amino acids
Theoretical weight: 8.27 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni

Ligands and Environments

4 bound ligands:
Ligand VP5 1 x VP5
Ligand EDO 3 x EDO
Ligand NAG 1 x NAG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 44.436Å b: 71.08Å c: 78.232Å
α: 90° β: 98.433° γ: 90°
R-values:
R R work R free
0.182 0.18 0.216
Expression system: Trichoplusia ni

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Citations

1 citations in other articles

The Uptake of Heparanase into Mast Cells Is Regulated by Its Enzymatic Activity to Degrade Heparan Sulfate.
Shi et al. (2024)