3PS2 | pdb_00003ps2

Crystal structure of the Escherichia Coli LPXC/LPC-012 complex

• PDB DOI: https://doi.org/10.2210/pdb3PS2/pdb

• Classification: HYDROLASE/ANTIBIOTIC
• Organism(s): Escherichia coli IHE3034
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-11-30 Released: 2011-01-19 
• Deposition Author(s): Lee, C.-J., Zhou, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Syntheses, structures and antibiotic activities of LpxC inhibitors based on the diacetylene scaffold.

Liang, X., Lee, C.J., Chen, X., Chung, H.S., Zeng, D., Raetz, C.R., Li, Y., Zhou, P., Toone, E.J.

(2011) Bioorg Med Chem 19: 852-860

• PubMed: 21194954 
• DOI: https://doi.org/10.1016/j.bmc.2010.12.017
• Primary Citation Related Structures: 
  3PS1, 3PS2, 3PS3


• PubMed Abstract: 
  

  Compounds inhibiting LpxC in the lipid A biosynthetic pathway are promising leads for novel antibiotics against multidrug-resistant Gram-negative pathogens. We report the syntheses and structural and biochemical characterizations of LpxC inhibitors based on a diphenyl-diacetylene (1,4-diphenyl-1,3-butadiyne) threonyl-hydroxamate scaffold. These studies provide a molecular interpretation for the differential antibiotic activities of compounds with a substituted distal phenyl ring as well as the absolute stereochemical requirement at the C2, but not C3, position of the threonyl group.

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Organizational Affiliation: 
• Department of Chemistry, Jilin University, Changchun, PR China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.78 kDa 
• Atom Count: 2,536 
• Modeled Residue Count: 300 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A	300	Escherichia coli IHE3034	Mutation(s): 0  Gene Names: ECOK1_0097, ENVA, lpxC EC: 3.5.1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZH4	C [auth A]	4-[4-(3-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3R)-3-hydroxy-1-nitroso-1-oxobutan-2-yl]benzamide C21 H17 N3 O4 HOPLGMFTTVLMDZ-KUHUBIRLSA-N
UKW	D [auth A]	4-ethynyl-N-[(1S,2R)-2-hydroxy-1-(oxocarbamoyl)propyl]benzamide C13 H12 N2 O4 JJXZDQZGPLQGCP-KCJUWKMLSA-N
SO4	H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.449	α = 90
b = 107.449	β = 90
c = 53.422	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Lee, C.-J., Zhou, P.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations