› 6pkg

X-ray diffraction
2.8Å resolution

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

Released:
DOI: 10.2210/pdb6pkg/pdb
PDB entry 6pkg coloured by chain, front view.
PDB entry 6pkg coloured by chain, side view.
PDB entry 6pkg 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 Chains: A, B
Molecule details ›
Chains: A, B
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
4 bound ligands:
Ligand NAG 3 x NAG
Ligand IOD 48 x IOD
Ligand I2I 15 x I2I
Ligand P6G 1 x P6G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P41212
Unit cell:
a: 124.356Å b: 124.356Å c: 278.792Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.183 0.208
Expression system: Spodoptera frugiperda

Quick links

Citations

3 citation in other articles

Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages.
Evseev et al. (2023)
2 more