Acid-beta-glucosidase low pH, glycerol bound

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease.

Lieberman, R.L.Wustman, B.A.Huertas, P.Powe, A.C.Pine, C.W.Khanna, R.Schlossmacher, M.G.Ringe, D.Petsko, G.A.

(2007) Nat Chem Biol 3: 101-107

  • DOI: https://doi.org/10.1038/nchembio850
  • Primary Citation of Related Structures:  
    2NSX, 2NT0, 2NT1

  • PubMed Abstract: 

    Gaucher disease results from mutations in the lysosomal enzyme acid beta-glucosidase (GCase). Although enzyme replacement therapy has improved the health of some affected individuals, such as those with the prevalent N370S mutation, oral treatment with pharmacological chaperones may be therapeutic in a wider range of tissue compartments by restoring sufficient activity of endogenous mutant GCase. Here we demonstrate that isofagomine (IFG, 1) binds to the GCase active site, and both increases GCase activity in cell lysates and restores lysosomal trafficking in cells containing N370S mutant GCase. We also compare the crystal structures of IFG-bound GCase at low pH with those of glycerol-bound GCase at low pH and apo-GCase at neutral pH. Our data indicate that IFG induces active GCase, which is secured by interactions with Asn370. The design of small molecules that stabilize substrate-bound conformations of mutant proteins may be a general therapeutic strategy for diseases caused by protein misfolding and mistrafficking.

  • Organizational Affiliation

    Structural Neurology Lab, Brigham and Women's Hospital and Harvard Medical School, 77 Ave Louis Pasteur, Boston, Massachusetts 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
497Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), 2.4.1 (UniProt), 3.2.1 (UniProt), (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04062 (Homo sapiens)
Explore P04062 
Go to UniProtKB:  P04062
PHAROS:  P04062
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04062
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
FA [auth D],
L [auth B],
M [auth B],
W [auth C]
C8 H15 N O6
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
GA [auth D]
H [auth A]
HA [auth D]
F [auth A],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
JA [auth D],
KA [auth D],
LA [auth D],
MA [auth D],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
X [auth C],
Y [auth C],
Z [auth C]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
J [auth A],
K [auth A],
NA [auth D],
OA [auth D],
PA [auth D],
T [auth B],
U [auth B],
V [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.941α = 90
b = 91.759β = 110.96
c = 152.81γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary