2V3D

ACID-BETA-GLUCOSIDASE WITH N-BUTYL-DEOXYNOJIRIMYCIN

Structural Biology Knowledgebase: 2V3D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.154

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2V3D

Classification: HYDROLASE

Total Structure Weight: 116073.62

Macromolecule Entities
Molecule Chains Length Organism Details
GLUCOSYLCERAMIDASE A, B 505 Homo sapiens EC#: 3.2.1.45 IUBMB
Mutation: R495H
Details: NB-DNJ INHIBITOR 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
NAG
Query on NAG

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

A, B (2R,3R,4R,5S)-1-BUTYL-2-(HYDROXYMETHYL)PIPERIDINE- 3,4,5-TRIOL
C10 H21 N O4
UQRORFVVSGFNRO-UTINFBMNSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

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

A, B ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NBV IC50: 259000 - 400000 nM (99) BindingDB
Ki: 116000 nM (99) BindingDB

Ki: 116000 nM  BindingMOAD
Ki: 116000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.154
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 67.99 α = 90.00
b = 97.21 β = 102.91
c = 82.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-06-17
  • Released Date: 2007-08-14
  • 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