2XWD

X-RAY STRUCTURE OF ACID-BETA-GLUCOSIDASE WITH 5N,6O-(N'-(N-OCTYL)IMINO)NOJIRIMYCIN IN THE ACTIVE SITE

Structural Biology Knowledgebase: 2XWD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.150

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2XWD

Classification: HYDROLASE

Total Structure Weight: 116238.75

Macromolecule Entities
Molecule Chains Length Organism Details
GLUCOSYLCERAMIDASE A, B 505 Homo sapiens EC#: 3.2.1.45 IUBMB
Mutation: R495H
Gene Name(s): GBA Gene View GC Gene View GLUC

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

A, B (3Z,5S,6R,7S,8R,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4- a]pyridine-5,6,7,8-tetrol
C15 H28 N2 O5
QJILQIWQVOAQBB-KRIYVDMXSA-N
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)
BMA
Query on BMA

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

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-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 %)
LGS N/A in BindingDB
N/A in BindingMoad
Ki: 110 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.150
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.04 α = 90.00
b = 96.62 β = 103.69
c = 83.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-11-01
  • Released Date: 2011-09-14
  • Deposition author(s): Brumshtein, B., Aguilar-Moncayo, M., Benito, J.M., Ortiz Mellet, C., Garcia Fernandez, J.M., Silman, I., Shaaltiel, Y., Sussman, J.L., Futerman, A.H.

Revision History

No revisions since initial release