› 4do5

X-ray diffraction
1.51Å resolution

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase

Released:
DOI: 10.2210/pdb4do5/pdb
PDB entry 4do5 coloured by chain, front view.
PDB entry 4do5 coloured by chain, side view.
PDB entry 4do5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Pharmacological chaperones for human α-N-acetylgalactosaminidase.
Clark NE, Metcalf MC, Best D, Fleet GW, Garman SC
Proc Natl Acad Sci U S A 109 17400-5 (2012)
PMID: 23045655

Function and Biology Details

Reaction catalysed: 
Cleavage of non-reducing alpha-(1->3)-N-acetylgalactosamine residues from human blood group A and AB mucin glycoproteins, Forssman hapten and blood group A lacto series glycolipids
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147860 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Alpha-N-acetylgalactosaminidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 400 amino acids
Theoretical weight: 45.58 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P17050 (Residues: 18-411; Coverage: 100%)
Gene name: NAGA
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand NAG 2 x NAG
Ligand DGJ 2 x DGJ
Ligand CIT 2 x CIT
Ligand GOL 14 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: C2
Unit cell:
a: 154.352Å b: 114.513Å c: 68.553Å
α: 90° β: 95.64° γ: 90°
R-values:
R R work R free
0.16 0.159 0.178
Expression system: Trichoplusia ni

Quick links

Citations

7 review citations

Lysosomal storage diseases.
Ferreira et al. (2017)
6 more

2 mentions without citation

Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.
Williamson et al. (2020)
1 more