› 8ohq

X-ray diffraction
1.7Å resolution

Crystal structure of human heparanase in complex with competitive inhibitor derrived from siastatin B

Released:
DOI: 10.2210/pdb8ohq/pdb
PDB entry 8ohq coloured by chain, front view.
PDB entry 8ohq coloured by chain, side view.
PDB entry 8ohq 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

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:

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: AAA
Molecule details ›
Chain: AAA
Length: 385 amino acids
Theoretical weight: 43.33 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9Y251 (Residues: 160-543; 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: 74 amino acids
Theoretical weight: 8.27 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
Carbohydrate polymer
4 bound ligands:
Ligand NAG 4 x NAG
Ligand EDO 3 x EDO
Ligand CL 3 x CL
Ligand VGO 1 x VGO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 46.11Å b: 70.92Å c: 78.56Å
α: 90° β: 95.53° γ: 90°
R-values:
R R work R free
0.176 0.174 0.208
Expression system: Trichoplusia ni

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