3W0T | pdb_00003w0t

Human Glyoxalase I with an N-hydroxypyridone derivative inhibitor

PDB DOI: https://doi.org/10.2210/pdb3W0T/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.197 (Depositor), 0.201 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 86.75 kDa
Atom Count: 6,794
Modeled Residue Count: 710
Deposited Residue Count: 748
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoylglutathione lyase	A, B, C, D	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
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HPU Query on HPU Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], J [auth B], L [auth C], O [auth D]	N-[3-(1-hydroxy-6-oxo-4-phenyl-1,6-dihydropyridin-2-yl)phenyl]methanesulfonamide C₁₈ H₁₆ N₂ O₄ S MDYXMYBWSBAIMZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain N [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain N [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	H [auth B], I [auth B], N [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A], G [auth B], K [auth C], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.197 (Depositor), 0.201 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.57	α = 90
b = 81.03	β = 90.13
c = 68.62	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-11-06

Deposition Author(s):

Fukami, T.A.

Irie, M.

Matsuura, T.

Revision History (Full details and data files)

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

3W0T | pdb_00003w0t

Human Glyoxalase I with an N-hydroxypyridone derivative inhibitor

Literature

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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