4OPN | pdb_00004opn

Crystal structure of mouse glyoxalase I complexed with mAH

PDB DOI: https://doi.org/10.2210/pdb4OPN/pdb

Classification: LYASE/LYASE INHIBITOR
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-02-06 Released: 2015-02-11
Deposition Author(s): Zhai, J., Zhang, L., Yuan, M., Zhang, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.231 (Depositor), 0.232 (DCC)
R-Value Work:
0.177 (Depositor), 0.181 (DCC)
R-Value Observed:
0.180 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Reversible Inhibition of Glyoxalase I: Synthesis and Activity Evaluation

Shi, Q., Zhai, J., Zheng, Z., Hu, X.

To be published.

Macromolecule Content

Total Structure Weight: 42.7 kDa
Atom Count: 3,093
Modeled Residue Count: 346
Deposited Residue Count: 368
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoylglutathione lyase	A, B	184	Mus musculus	Mutation(s): 0 Gene Names: Glo1 EC: 4.4.1.5
UniProt
Find proteins for Q9CPU0 (Mus musculus) Explore Q9CPU0 Go to UniProtKB: Q9CPU0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CPU0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZBF Query on ZBF Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	L-gamma-glutamyl-N-(3-ethynylphenyl)-N-hydroxy-L-glutaminylglycine C₂₀ H₂₄ N₄ O₈ DNHXPPJCZZCCCC-GJZGRUSLSA-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 C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	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]

Binding Affinity Annotations
ID	Source	Binding Affinity
ZBF	BindingDB: 4OPN	Ki: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.231 (Depositor), 0.232 (DCC)
R-Value Work: 0.177 (Depositor), 0.181 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.559	α = 90
b = 65.084	β = 101.29
c = 64.885	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
PHENIX	refinement
CrysalisPro	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-02-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-11
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.