› 1ktc

X-ray diffraction
2.4Å resolution

The Structure of alpha-N-Acetylgalactosaminidase

Released:
DOI: 10.2210/pdb1ktc/pdb
PDB entry 1ktc coloured by chain, front view.
PDB entry 1ktc coloured by chain, side view.
PDB entry 1ktc coloured by chain, top view.
Source organism: Gallus gallus
Primary publication:
The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.
Garman SC, Hannick L, Zhu A, Garboczi DN
Structure 10 425-34 (2002)
PMID: 12005440

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 domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187449 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Alpha-N-acetylgalactosaminidase Chain: A
Molecule details ›
Chain: A
Length: 405 amino acids
Theoretical weight: 45.59 KDa
Source organism: Gallus gallus
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q90744 (Residues: 1-405; Coverage: 100%)
Gene name: NAGA
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
5 bound ligands:
Ligand NAG 2 x NAG
Ligand NGA 1 x NGA
Ligand SO4 5 x SO4
Ligand GOL 10 x GOL
Ligand ACY 2 x ACY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9B
Spacegroup: P43212
Unit cell:
a: 72.93Å b: 72.93Å c: 176.413Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.216 0.231
Expression system: Komagataella pastoris

Quick links

Citations

5 review citations

Glycosidase mechanisms.
Vasella et al. (2002)
4 more

1 mention without citation

A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27.
Ichinose et al. (2009)