3W0U

human Glyoxalase I with an N-hydroxypyridone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3W0U/pdb

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


• Deposited: 2012-11-02 Released: 2013-11-06 
• Deposition Author(s): Fukami, T.A., Irie, M., Matsuura, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

N-Hydroxypyridone-based glyoxalase I inhibitors mimicking binding interactions of the substrate

Koyano, H., Aoki, T., Yamamoto, S., Kobayashi, T., Miura, T., Ohara, K., Fukami, T.A., Irie, M., Sakamoto, 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)

Macromolecule Content

• Total Structure Weight: 43.2 kDa 
• Atom Count: 2,979 
• Modelled Residue Count: 350 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoylglutathione lyase	A, B	187	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
HPW	E [auth A], F [auth B]	N-[3-(1-Hydroxy-6-oxo-4-phenyl-1,6-dihydro-pyridin-2-yl)-5-methanesulfonylamino-phenyl]-methanesulfonamide C19 H19 N3 O6 S2 AKWZUDBNQVPNBK-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.17	α = 90
b = 67.38	β = 90
c = 68.48	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-06 
Deposition Author(s): Fukami, T.A., Irie, M., Matsuura, T.

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description