2V3E

ACID-BETA-GLUCOSIDASE WITH N-NONYL-DEOXYNOJIRIMYCIN

Structural Biology Knowledgebase: 2V3E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.160

Literature

Macromolecules
Sequence Display for 2V3E

Classification: HYDROLASE

Total Structure Weight: 115635.37

Macromolecule Entities
Molecule Chains Length Organism Details
GLUCOSYLCERAMIDASE A, B 505 Homo sapiens EC#: 3.2.1.45 IUBMB
Mutation: R495H
Details: NN-DNJ IN THE ACTIVE SITE
Gene Name(s): GBA Gene View GC Gene View GLUC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NND
Query on NND

A, B (2R,3R,4R,5S)-2-(HYDROXYMETHYL)-1-NONYLPIPERIDINE- 3,4,5-TRIOL
N-NONYL-DEOXYNOJIRIMYCIN (Synonym)
C15 H31 N O4
FTSCEGKYKXESFF-LXTVHRRPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

A, B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A, B ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NND IC50: 300 - 1500 nM (99) BindingDB
Ki: 300 - 1300 nM (99) BindingDB

Ki: 300 nM  BindingMOAD
Ki: 300 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.160
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.00 α = 90.00
b = 97.65 β = 102.75
c = 82.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-06-17
  • Released Date: 2007-08-21
  • Deposition author(s): Brumshtein, B., Greenblatt, H.M., Butters, T.D., Shaaltiel, Y., Aviezer, D., Silman, I., Futerman, A.H., Sussman, J.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4