› 7rg8

X-ray diffraction
1.3Å resolution

Crystal Structure of a Stable Heparanase Mutant

Released:
DOI: 10.2210/pdb7rg8/pdb
PDB entry 7rg8 coloured by chain, front view.
PDB entry 7rg8 coloured by chain, side view.
PDB entry 7rg8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Computational design and experimental characterisation of a stable human heparanase variant.
Whitefield C, Hong N, Mitchell JA, Jackson CJ
OpenAccess logo RSC Chem Biol 3 341-349 (2022)
PMID: 35382258

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: 387 amino acids
Theoretical weight: 43.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q9Y251 (Residues: 157-543; 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: 92 amino acids
Theoretical weight: 10.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q9Y251 (Residues: 36-109; Coverage: 15%)
Gene names: HEP, HPA, HPA1, HPR1, HPSE, HPSE1, HSE1

Ligands and Environments

2 bound ligands:
Ligand ACT 1 x ACT
Ligand NA 4 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 59.785Å b: 76.094Å c: 124.432Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.144 0.143 0.165
Expression system: Escherichia coli K-12

Quick links

Citations

1 review citation

Biocatalytic Approaches to Building Blocks for Enzymatic and Chemical Glycan Synthesis.
Dolan et al. (2023)
1 other article

1 mention without citation

Computational design and experimental characterisation of a stable human heparanase variant.
Whitefield et al. (2022)