› 5l9z

X-ray diffraction
1.57Å resolution

Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted glucuronic acid configured aziridine probe JJB355

Released:
DOI: 10.2210/pdb5l9z/pdb
PDB entry 5l9z coloured by chain, front view.
PDB entry 5l9z coloured by chain, side view.
PDB entry 5l9z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Activity-based probes for functional interrogation of retaining β-glucuronidases.
Wu L, Jiang J, Jin Y, Kallemeijn WW, Kuo CL, Artola M, Dai W, van Elk C, van Eijk M, van der Marel GA, Codée JDC, Florea BI, Aerts JMFG, Overkleeft HS, Davies GJ
Nat Chem Biol 13 867-873 (2017)
PMID: 28581485

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: 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

4 bound ligands:
Ligand NAG 4 x NAG
Ligand EDO 7 x EDO
Ligand CL 3 x CL
Ligand GUX 1 x GUX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 46.19Å b: 71.05Å c: 78.69Å
α: 90° β: 95.2° γ: 90°
R-values:
R R work R free
0.167 0.166 0.193
Expression system: Trichoplusia ni

Quick links

Citations

16 review citations

Opposing Functions of Heparanase-1 and Heparanase-2 in Cancer Progression.
Vlodavsky et al. (2018)
15 more

1 mention without citation

Spatiotemporal identification of druggable binding sites using deep learning.
Kozlovskii et al. (2020)