2NSX

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

Structural Biology Knowledgebase: 2NSX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.191

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2NSX

Classification: Hydrolase

Total Structure Weight: 225877.22

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 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

A, C GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
IFM
Query on IFM

B, D 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
Afegostat, isofagomine, (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE- 3,4-DIOL (Synonym)
C6 H13 N O3
QPYJXFZUIJOGNX-HSUXUTPPSA-N
Ligand Explorer
 
JSmol
NAG
Query on NAG

B, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol
NDG
Query on NDG

A, C 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IFM IC50: 30 - 31000 nM (90 - 99) BindingDB
Ki: 5 - 110 nM (99) BindingDB

IC50: 59 nM  BindingMOAD
IC50: 63 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.191
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 108.97 α = 90.00
b = 92.22 β = 110.94
c = 152.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-11-06
  • Released Date: 2006-12-26
  • Deposition author(s): Lieberman, R.L., Petsko, G.A., Ringe, D.

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