› 6pkh

X-ray diffraction
1.6Å resolution

Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain auto-inhibited by pro-peptide

Released:
DOI: 10.2210/pdb6pkh/pdb
PDB entry 6pkh coloured by chain, front view.
PDB entry 6pkh coloured by chain, side view.
PDB entry 6pkh coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Crystal Structure of the Mannose-6-Phosphate Uncovering Enzyme.
Gorelik A, Illes K, Nagar B
Structure 28 426-436.e3 (2020)
PMID: 32109365

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123350 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
EGF-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 321 amino acids
Theoretical weight: 35.63 KDa
Source organism: Danio rerio
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: F1QSF9 (Residues: 45-355; Coverage: 51%)
Gene name: nagpa
Sequence domains: Phosphodiester glycosidase

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P41212
Unit cell:
a: 73.954Å b: 73.954Å c: 109.288Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.14 0.138 0.173
Expression system: Spodoptera frugiperda

Quick links

Citations

3 citation in other articles

Mannose-6-phosphate glycan for lysosomal targeting: various applications from enzyme replacement therapy to lysosome-targeting chimeras.
Seo et al. (2022)
2 more