2WCG

X-RAY STRUCTURE OF ACID-BETA-GLUCOSIDASE WITH N-OCTYL(CYCLIC GUANIDINE)-NOJIRIMYCIN IN THE ACTIVE SITE

Structural Biology Knowledgebase: 2WCG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.135

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2WCG

Classification: HYDROLASE

Total Structure Weight: 116541.89

Macromolecule Entities
Molecule Chains Length Organism Details
GLUCOSYLCERAMIDASE A, B 505 Homo sapiens EC#: 3.2.1.45 IUBMB
Fragment: RESIDUES 40-536
Gene Name(s): GBA Gene View GC Gene View GLUC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MT5
Query on MT5

A, B N-[(3E,5R,6R,7S,8R,8AR)-5,6,7,8-TETRAHYDROXYHEXAHYDROIMIDAZO[1,5- A]PYRIDIN-3(2H)-YLIDENE]OCTAN-1-AMINIUM
C15 H30 N3 O4
DGGJYTDCPYQDLL-RKQHYHRCSA-O
Ligand Explorer
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FU4
Query on FU4

A, B 2,6-ANHYDRO-1-DEOXY-D-GALACTITOL
C6 H12 O4
KBVSUNBCTPQWJL-KCDKBNATSA-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)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MT5 N/A in BindingDB
IC50: 4000 nM  BindingMOAD
Ki: 420 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.135
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.31 α = 90.00
b = 96.83 β = 104.34
c = 83.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-03-12
  • Released Date: 2009-11-24
  • Deposition author(s): Brumshtein, B., Aguilar, M., Garcia-Moreno, M.I., Mellet, C.O., Garcia-Fernandez, J.M., Silman, I., Shaaltiel, Y., Aviezer, D., Sussman, J.L., Futerman, A.H.

Revision History

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