3THD | pdb_00003thd

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.228 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

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 Biological Chem 287: 1801-1812

  • DOI: https://doi.org/10.1074/jbc.M111.293795
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 300.26 kDa 
  • Atom Count: 21,969 
  • Modeled Residue Count: 2,414 
  • Deposited Residue Count: 2,616 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, B, C, D
654Homo sapiensMutation(s): 0 
Gene Names: GLB1ELNR1
EC: 3.2.1.23
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
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P16278-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

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]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
DGJ

Query on DGJ



Download:Ideal Coordinates CCD File
DA [auth C],
J [auth A],
NA [auth D],
T [auth B]
(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol
C6 H13 N O4
LXBIFEVIBLOUGU-DPYQTVNSSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
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]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

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]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
CA [auth C],
I [auth A],
MA [auth D],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.228 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
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
MOLREPphasing
REFMACrefinement
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
  • Version 1.4: 2024-11-13
    Changes: Structure summary