Crystal structure of human beta-galactosidase in complex with 1-deoxygalactonojirimycin

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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This is version 1.3 of the entry. See complete history


Crystal structure of human beta-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases

Ohto, U.Usui, K.Ochi, T.Yuki, K.Satow, Y.Shimizu, T.

(2012) J Biol Chem 287: 1801-1812

  • DOI: https://doi.org/10.1074/jbc.M111.293795
  • Primary Citation of Related Structures:  
    3THC, 3THD

  • PubMed Abstract: 

    G(M1) gangliosidosis and Morquio B are autosomal recessive lysosomal storage diseases associated with a neurodegenerative disorder or dwarfism and skeletal abnormalities, respectively. These diseases are caused by deficiencies in the lysosomal enzyme β-d-galactosidase (β-Gal), which lead to accumulations of the β-Gal substrates, G(M1) ganglioside, and keratan sulfate. β-Gal is an exoglycosidase that catalyzes the hydrolysis of terminal β-linked galactose residues. This study shows the crystal structures of human β-Gal in complex with its catalytic product galactose or with its inhibitor 1-deoxygalactonojirimycin. Human β-Gal is composed of a catalytic TIM barrel domain followed by β-domain 1 and β-domain 2. To gain structural insight into the molecular defects of β-Gal in the above diseases, the disease-causing mutations were mapped onto the three-dimensional structure. Finally, the possible causes of the diseases are discussed.

  • Organizational Affiliation

    From the Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
654Homo sapiensMutation(s): 0 
Gene Names: GLB1ELNR1
UniProt & NIH Common Fund Data Resources
Find proteins for P16278 (Homo sapiens)
Explore P16278 
Go to UniProtKB:  P16278
PHAROS:  P16278
GTEx:  ENSG00000170266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16278
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
E [auth A]
F [auth A]
G [auth A]
AA [auth C],
BA [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
IA [auth D],
JA [auth D],
KA [auth D],
LA [auth D],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
Y [auth C],
Z [auth C]
C8 H15 N O6
Query on DGJ

Download Ideal Coordinates CCD File 
DA [auth C],
J [auth A],
NA [auth D],
T [auth B]
C6 H13 N O4
Query on SO4

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EA [auth C]
FA [auth C]
K [auth A]
L [auth A]
OA [auth D]
EA [auth C],
FA [auth C],
K [auth A],
L [auth A],
OA [auth D],
PA [auth D],
U [auth B],
V [auth B]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
GA [auth C]
HA [auth C]
M [auth A]
N [auth A]
QA [auth D]
GA [auth C],
HA [auth C],
M [auth A],
N [auth A],
QA [auth D],
RA [auth D],
W [auth B],
X [auth B]
C2 H6 O2
Query on CL

Download Ideal Coordinates CCD File 
CA [auth C],
I [auth A],
MA [auth D],
S [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
DGJ BindingDB:  3THD Ki: min: 4.47e+4, max: 6.18e+4 (nM) from 3 assay(s)
IC50: 9.00e+4 (nM) from 1 assay(s)
PDBBind:  3THD IC50: 9.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.792α = 90
b = 115.996β = 92.22
c = 140.327γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary