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
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Ligand Structure Quality Assessment

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Literature

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

Ando, K., Yokoyama, H.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L5R (Subject of Investigation/LOI) Query on A1L5R Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	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		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.