5e8m

X-ray diffraction
1.75Å resolution

Crystal structure of human heparanase

Released:
Source organism: Homo sapiens

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195099 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Heparanase 50 kDa subunit Chain: A
Molecule details ›
Chain: A
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: B
Molecule details ›
Chain: B
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

Carbohydrate polymer : NEW Components: NAG, FUC
3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21
Unit cell:
a: 46.765Å b: 70.972Å c: 78.948Å
α: 90° β: 94.17° γ: 90°
R-values:
R R work R free
0.166 0.164 0.2
Expression system: Trichoplusia ni