2ZOX

Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase

• PDB DOI: https://doi.org/10.2210/pdb2ZOX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-06-17 Released: 2008-09-30 
• Deposition Author(s): Noguchi, J., Hayashi, Y., Baba, Y., Okino, N., Kimura, M., Ito, M., Kakuta, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.226 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.26 kDa 
• Atom Count: 4,092 
• Modelled Residue Count: 466 
• Deposited Residue Count: 469 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosolic beta-glucosidase	A	469	Homo sapiens	Mutation(s): 1  Gene Names: GBA3, CBG, CBGL1 EC: 3.2.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H227 (Homo sapiens) Explore Q9H227  Go to UniProtKB:  Q9H227
PHAROS:  Q9H227

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PNG	C [auth A]	4-nitrophenyl alpha-D-glucopyranoside C12 H15 N O8 IFBHRQDFSNCLOZ-ZIQFBCGOSA-N
OLA	H [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PLM	G [auth A], I [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.226 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.12	α = 90
b = 82.529	β = 90
c = 91.673	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Noguchi, J., Hayashi, Y., Baba, Y., Okino, N., Kimura, M., Ito, M., Kakuta, Y.

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.3: 2021-11-10
  Changes: Database references, Structure summary
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description