› 6zdm

X-ray diffraction
1.71Å resolution

Crystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide

Released:
DOI: 10.2210/pdb6zdm/pdb
PDB entry 6zdm coloured by chain, front view.
PDB entry 6zdm coloured by chain, side view.
PDB entry 6zdm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into heparanase activity using a fluorogenic heparan sulfate disaccharide.
Wu L, Wimmer N, Davies GJ, Ferro V
Chem Commun (Camb) 56 13780-13783 (2020)
PMID: 33073275

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->4)-beta-D-glycosidic bonds of heparan sulfate chains in heparan sulfate proteoglycan
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

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: 389 amino acids
Theoretical weight: 43.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9Y251 (Residues: 158-543; Coverage: 76%)
Gene names: HEP, HPA, HPA1, HPR1, HPSE, HPSE1, HSE1
Sequence domains: Glycosyl hydrolase family 79, N-terminal domain
Heparanase 8 kDa subunit Chain: BBB
Molecule details ›
Chain: BBB
Length: 77 amino acids
Theoretical weight: 8.54 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9Y251 (Residues: 36-109; Coverage: 15%)
Gene names: HEP, HPA, HPA1, HPR1, HPSE, HPSE1, HSE1

Ligands and Environments

4 bound ligands:
Ligand NAG 1 x NAG
Ligand EDO 1 x EDO
Ligand QG2 1 x QG2
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 44.974Å b: 70.856Å c: 78.455Å
α: 90° β: 97.128° γ: 90°
R-values:
R R work R free
0.182 0.179 0.241
Expression system: Trichoplusia ni

Quick links

Citations

1 review citation

From Cancer to COVID-19: A Perspective on Targeting Heparan Sulfate-Protein Interactions.
Chhabra et al. (2021)
1 other article

2 mentions without citation

Structural Insights into Pixatimod (PG545) Inhibition of Heparanase, a Key Enzyme in Cancer and Viral Infections.
Chhabra et al. (2022)
1 more