› 3igu

X-ray diffraction
2.15Å resolution

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

Released:
DOI: 10.2210/pdb3igu/pdb
PDB entry 3igu coloured by chain, front view.
PDB entry 3igu coloured by chain, side view.
PDB entry 3igu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases.
Clark NE, Garman SC
J Mol Biol 393 435-47 (2009)
PMID: 19683538

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 (4 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
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
3 bound ligands:
Ligand GOL 15 x GOL
Ligand 7JZ 2 x 7JZ
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: C2
Unit cell:
a: 151.612Å b: 113.649Å c: 68.415Å
α: 90° β: 96.14° γ: 90°
R-values:
R R work R free
0.166 0.164 0.199
Expression system: Trichoplusia ni

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Citations

6 review citations

Emerging novel concept of chaperone therapies for protein misfolding diseases.
Suzuki Y. (2014)
5 more

1 mention without citation

The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases.
Clark et al. (2009)