› 2gk1

X-ray diffraction
3.25Å resolution

X-ray crystal structure of NGT-bound HexA

Released:
DOI: 10.2210/pdb2gk1/pdb
PDB entry 2gk1 coloured by chain, front view.
PDB entry 2gk1 coloured by chain, side view.
PDB entry 2gk1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystallographic structure of human beta-hexosaminidase A: interpretation of Tay-Sachs mutations and loss of GM2 ganglioside hydrolysis.
Lemieux MJ, Mark BL, Cherney MM, Withers SG, Mahuran DJ, James MN
J Mol Biol 359 913-29 (2006)
PMID: 16698036

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero decamer
Assembly name:
PDBe Complex ID:
PDB-CPX-139262 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (7 distinct):
Beta-hexosaminidase subunit alpha Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 52 amino acids
Theoretical weight: 6.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P06865 (Residues: 23-74; Coverage: 10%)
Gene name: HEXA
Sequence domains: beta-acetyl hexosaminidase like
Beta-hexosaminidase subunit alpha Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 440 amino acids
Theoretical weight: 50.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P06865 (Residues: 89-528; Coverage: 87%)
Gene name: HEXA
Sequence domains:
Structure domains: Glycosidases
Beta-hexosaminidase subunit beta Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 58 amino acids
Theoretical weight: 6.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P07686 (Residues: 50-107; Coverage: 11%)
Gene names: HCC7, HEXB
Sequence domains: beta-acetyl hexosaminidase like
Beta-hexosaminidase subunit beta chain B Chains: M, O, Q, S
Molecule details ›
Chains: M, O, Q, S
Length: 190 amino acids
Theoretical weight: 21.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P07686 (Residues: 122-311; Coverage: 37%)
Gene names: HCC7, HEXB
Sequence domains:
Beta-hexosaminidase subunit beta chain A Chains: N, P, R, T
Molecule details ›
Chains: N, P, R, T
Length: 237 amino acids
Theoretical weight: 27.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P07686 (Residues: 316-552; Coverage: 46%)
Gene names: HCC7, HEXB
Sequence domains: Glycosyl hydrolase family 20, catalytic domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NGT 8 x NGT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: C2
Unit cell:
a: 322.246Å b: 109.796Å c: 132.764Å
α: 90° β: 91.48° γ: 90°
R-values:
R R work R free
0.277 0.274 0.322

Quick links

Citations

13 review citations

Mechanistic insights into glycosidase chemistry.
Vocadlo et al. (2008)
12 more

7 mentions without citation

Lending a helping hand, screening chemical libraries for compounds that enhance beta-hexosaminidase A activity in GM2 gangliosidosis cells.
Tropak et al. (2007)
6 more