29AI | pdb_000029ai

Crystal structure of EcLpxC complexed with compound 7a

PDB DOI: https://doi.org/10.2210/pdb29AI/pdb

Classification: ANTIBIOTIC
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-03-03 Released: 2026-07-29
Deposition Author(s): Beaumont, E., Cade, I., Kopec, J., Martin, D.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.270 (Depositor), 0.269 (DCC)
R-Value Work:
0.245 (Depositor), 0.242 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of EcLpxC complexed with compound 7a

beaumont, E., Martin, D.

To be published.

Macromolecule Content

Total Structure Weight: 132.37 kDa
Atom Count: 9,228
Modeled Residue Count: 1,152
Deposited Residue Count: 1,160
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-acyl-N-acetylglucosamine deacetylase	A, B, C, D	290	Escherichia coli	Mutation(s): 0 Gene Names: lpxC, EcE24377A_0098 EC: 3.5.1.108
UniProt
Find proteins for A7ZHI7 (Escherichia coli O139:H28 (strain E24377A / ETEC)) Explore A7ZHI7 Go to UniProtKB: A7ZHI7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7ZHI7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1J1S( Subject of Investigation/LOI) Query on A1J1S Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	5-oxidanyl-4-[2-[4-[2-[4-[[(3-oxidanylcyclobutyl)amino]methyl]phenyl]ethynyl]phenyl]ethyl]-1~{H}-pyrimidin-6-one C₂₅ H₂₅ N₃ O₃ IEURYCLSYWGDNB-HZCBDIJESA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]