› 6pku

X-ray diffraction
1.95Å resolution

Guinea pig N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain (C51S C221S) in complex with N-acetyl-alpha-D-glucosamine (alpha-GlcNAc) and mannose 6-phosphate (M6P)

Released:
DOI: 10.2210/pdb6pku/pdb
PDB entry 6pku coloured by chain, front view.
PDB entry 6pku coloured by chain, side view.
PDB entry 6pku coloured by chain, top view.
Source organism: Cavia porcellus
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-124709 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphodiester glycosidase domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 300 amino acids
Theoretical weight: 32.49 KDa
Source organism: Cavia porcellus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: H0VTT5 (Residues: 55-343; Coverage: 54%)
Gene name: NAGPA
Sequence domains: Phosphodiester glycosidase

Ligands and Environments

3 bound ligands:
Ligand NDG 4 x NDG
Ligand M6P 4 x M6P
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 43.459Å b: 232.556Å c: 65.305Å
α: 90° β: 109.15° γ: 90°
R-values:
R R work R free
0.202 0.201 0.232
Expression system: Spodoptera frugiperda

Quick links

Citations

1 review citation

The host mannose-6-phosphate pathway and viral infection.
Liu et al. (2024)
3 other articles