3GXF

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

Structural Biology Knowledgebase: 3GXF SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3GXF

Classification: hydrolase

Total Structure Weight: 230281.40

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

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
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

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

A, B, C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IFM IC50: 30 - 31000 nM (90 - 99) BindingDB
Ki: 5 - 110 nM (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
  • Electron Density Server: EDS EDS

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

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4