› 5la7

X-ray diffraction
1.94Å resolution

Crystal structure of human proheparanase, in complex with glucuronic acid configured aziridine probe JJB355

Released:
DOI: 10.2210/pdb5la7/pdb
PDB entry 5la7 coloured by chain, front view.
PDB entry 5la7 coloured by chain, side view.
PDB entry 5la7 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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195098 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Heparanase Chain: A
Molecule details ›
Chain: A
Length: 509 amino acids
Theoretical weight: 57.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9Y251 (Residues: 36-543; Coverage: 100%)
Gene names: HEP, HPA, HPA1, HPR1, HPSE, HPSE1, HSE1
Sequence domains: Glycosyl hydrolase family 79, N-terminal domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
3 bound ligands:
Ligand NAG 3 x NAG
Ligand EDO 6 x EDO
Ligand 6S6 1 x 6S6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 50.41Å b: 88.02Å c: 118.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.223
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