2WCG

X-ray structure of acid-beta-glucosidase with N-octyl(cyclic guanidine)-nojirimycin in the active site


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

6-Amino-6-Deoxy-5,6-Di-N-(N'-Octyliminomethylidene)Nojirimycin: Synthesis, Biological Evaluation, and Crystal Structure in Complex with Acid Beta-Glucosidase.

Brumshtein, B.Aguilar-Moncayo, M.Garcia-Moreno, M.I.Ortiz Mellet, C.Garcia Fernandez, J.M.Silman, I.Shaaltiel, Y.Aviezer, D.Sussman, J.L.Futerman, A.H.

(2009) Chembiochem 10: 1480


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOSYLCERAMIDASE
A, B
505Homo sapiensMutation(s): 0 
Gene Names: GBA (GC, GLUC)
EC: 3.2.1.45
Find proteins for P04062 (Homo sapiens)
Go to Gene View: GBA
Go to UniProtKB:  P04062
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FUC
Query on FUC

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A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MT5
Query on MT5

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Download CCD File 
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 Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MT5IC50: 4000 nM BINDINGMOAD
MT5Ki: 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
Unit Cell:
Length (Å)Angle (°)
a = 68.311α = 90.00
b = 96.827β = 104.34
c = 83.234γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2017-11-15
    Type: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary