3VKK | pdb_00003vkk

Crystal Structure Of The Covalent Intermediate Of Human Cytosolic Beta-Glucosidase-mannose complex

• PDB DOI: https://doi.org/10.2210/pdb3VKK/pdb

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


• Deposited: 2011-11-17 Released: 2012-11-21 
• Deposition Author(s): Noguchi, J., Hayashi, Y., Okino, N., Ito, M., Kimura, M., Kakuta, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Structural basis for inhibition mechanism of human cytosolic beta-glucosidase by monnoside

Noguchi, J., Hayashi, Y., Okino, N., Ito, M., Kimura, M., Kakuta, Y.

To be published.

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: 54.84 kDa 
• Atom Count: 4,097 
• Modeled 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 (PDB Primary Data), 3.2.1.46 (UniProt), 3.2.1.45 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H227 (Homo sapiens) Explore Q9H227  Go to UniProtKB:  Q9H227
PHAROS:  Q9H227

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLA	G [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PLM	F [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
MAN	I [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
GOL	B [auth A], D [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.733	α = 90
b = 83.519	β = 90
c = 90.892	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Noguchi, J., Hayashi, Y., Okino, N., Ito, M., Kimura, M., Kakuta, Y.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary