8K08

Pq3-O-UGT2 with 20(S)-Ginsenoside Rh2

• PDB DOI: https://doi.org/10.2210/pdb8K08/pdb

• Classification: TRANSFERASE
• Organism(s): Panax quinquefolius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-07 Released: 2025-01-29 
• Deposition Author(s): Ji, Q.S., Liu, Y.R., Mei, K.R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.320 
• R-Value Work: 0.293 
• R-Value Observed: 0.294 

Starting Model: experimental

Literature

Structural Insights into the Substrate Recognition of Ginsenoside Glycosyltransferase Pq3-O-UGT2

Mei, K., Ji, Q., Liu, Y.

(2025) Adv Sci (Weinh) 

• DOI: https://doi.org/10.1002/advs.202413185

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 103.02 kDa 
• Atom Count: 6,329 
• Modelled Residue Count: 797 
• Deposited Residue Count: 910 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	455	Panax quinquefolius	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for A0A0M4ME80 (Panax quinquefolius) Explore A0A0M4ME80  Go to UniProtKB:  A0A0M4ME80

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8YG (Subject of Investigation/LOI)	C [auth A], D [auth B]	Ginsenoside Rh2 C36 H62 O8 CKUVNOCSBYYHIS-IRFFNABBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.320 
• R-Value Work: 0.293 
• R-Value Observed: 0.294 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.349	α = 90
b = 90.203	β = 90
c = 155.873	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
Coot	model building
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Ji, Q.S., Liu, Y.R., Mei, K.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release