9KEE | pdb_00009kee

human glyoxalase I (with C-ter His tag) in complex with licochalcone B, form 1

• PDB DOI: https://doi.org/10.2210/pdb9KEE/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-04 Released: 2025-11-12 
• Deposition Author(s): Ando, K., Yokoyama, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 

Starting Model: experimental

Literature

Crystal structures of glyoxalase I complexes with nature-derived inhibitors reveal flexible and multiple binding poses

Ando, K., Yokoyama, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.45 kDa 
• Atom Count: 2,965 
• Modeled Residue Count: 351 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoylglutathione lyase	A, B	192	Homo sapiens	Mutation(s): 0  Gene Names: GLO1 EC: 4.4.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q04760 (Homo sapiens) Explore Q04760  Go to UniProtKB:  Q04760
PHAROS:  Q04760 GTEx:  ENSG00000124767

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L5R (Subject of Investigation/LOI)	D [auth A], F [auth B]	1-(4-hydroxyphenyl)-3-[2-methoxy-3,4-bis(oxidanyl)phenyl]prop-2-en-1-one C16 H14 O5 DRDRYGIIYOPBBZ-YWEYNIOJSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.258	α = 90
b = 66.149	β = 99.688
c = 42.068	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Ando, K., Yokoyama, H.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22K06554

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release