3GXF

Crystal structure of acid-beta-glucosidase with isofagomine at neutral pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 3GXF

Classification: HYDROLASE

Total Structure Weight: 230278.47

Macromolecule Entities
Molecule Chains Length Organism Details
Glucosylceramidase A, B, C, D 497 Homo sapiens EC#: 3.2.1.45 IUBMB
Mutation: R495H
Gene Name(s): GBA Gene View GC Gene View GLUC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IFM
Query on IFM

B, D 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
4R,, (3R (Synonym)
C6 H13 N O3
QPYJXFZUIJOGNX-HSUXUTPPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C, D PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IFM IC50: 30 - 31000 nM (90 - 99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.178
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 110.31 α = 90.00
b = 92.01 β = 111.21
c = 152.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-04-02
  • Released Date: 2009-05-05
  • Deposition author(s): Lieberman, R.L.

Revision History

  • Version 1_0: 2009-05-05

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_2: 2017-11-01

    Type: Refinement description