9KL2 | pdb_00009kl2

Crystal structure of Pleurocybella porrigens lectin (PPL) in complex with GalNAc

• PDB DOI: https://doi.org/10.2210/pdb9KL2/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pleurocybella porrigens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-14 Released: 2025-11-19 
• Deposition Author(s): Adachi, D., Ishimoto, N., Kawabata, H., Mizutani, K., Park, S.-Y., Tame, J.R.H., Kamata, K.
• Funding Organization(s): Institute for Fermentation, Osaka

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: in silico

Literature

Crystal and Cryo-EM structure of PPL, a novel hexameric R-type lectin from the poisonous mushroom Pleurocybella porrigens.

Adachi, D., Ishimoto, N., Mizutani, K., Takahashi, K., Kubota, R., Kawabata, H., Park, S.Y., Vandebroek, L., Voet, A.R.D., Yamada, M., Ozeki, Y., Fujii, Y., Fujita, H., Tame, J.R.H., Kamata, K.

(2025) Glycobiology 36

• PubMed: 41342409 
• DOI: https://doi.org/10.1093/glycob/cwaf082
• Primary Citation of Related Structures:  
  9KL2, 9KL3


• PubMed Abstract: 
  

  Pleurocybella porrigens is a mushroom that grows widely around the temperate northern hemisphere, and was once considered edible, especially in Japan. Following a number of deaths in 2004, investigations revealed the presence of various toxins, including a lectin (PPL) that apparently survives cooking and enters the bloodstream via the stomach. We have cloned PPL and solved its structure by X-ray crystallography and cryo-EM. We report the sugar binding properties of this β-trefoil lectin, which has a novel hexameric structure.

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Organizational Affiliation: 
• Graduate School of Medical Life Science, Yokohama City University, Japan.
Department of Chemistry, Graduate School of Science, Chiba University, Japan.
Center of Quantum Life Science for Structural Therapeutics, Chiba University, Japan.
Department of Chemistry, KU Leuven, Belgium.
Graduate School of NanoBio Sciences, Yokohama City University, Japan.
Graduate School of Pharmaceutical Sciences, Nagasaki International University, Japan.
College of Science and Technology, Nihon University, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization, light scattering, electron microscopy

Macromolecule Content 

• Total Structure Weight: 44.72 kDa 
• Atom Count: 3,179 
• Modeled Residue Count: 398 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B, C	140	Pleurocybella porrigens	Mutation(s): 0
UniProt
Find proteins for B6ZK51 (Pleurocybella porrigens) Explore B6ZK51  Go to UniProtKB:  B6ZK51

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	D [auth A], F [auth B], H [auth C]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N
NO3	E [auth A], G [auth B], I [auth C]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.762	α = 90
b = 221.166	β = 90
c = 112.209	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Adachi, D., Ishimoto, N., Kawabata, H., Mizutani, K., Park, S.-Y., Tame, J.R.H., Kamata, K.

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Funding Organization	Location	Grant Number
Institute for Fermentation, Osaka	Japan	Y-2023-2-046

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release
  
• Version 1.1: 2025-12-17
  Changes: Database references
• Version 1.2: 2025-12-31
  Changes: Database references