4OKG

LpxC from P.aeruginosa with the inhibitor 6-(benzimidazol-1-yl)-5-[4-[2-[6-[(4-methylpiperazin-1-yl)methyl]-3-pyridyl]ethynyl]phenyl]pyridine-3-carbohydroxamic acid

• PDB DOI: https://doi.org/10.2210/pdb4OKG/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-01-22 Released: 2014-09-24 
• Deposition Author(s): Olivier, N.B., Lahiri, S.D., Prince, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.219 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Overexpression of Pseudomonas aeruginosa LpxC in the Presence of an Inhibitor in an acrB Deletion Escherichia coli strain for Structural Studies

Gao, N., McLeod, S.M., Hajec, H., Lahiri, S.D., Prince, D.B., Thresher, J., Whiteaker, J., Ross, P., Olivier, N.B., Doig, P.

(2014) Protein Express Purif 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 67.51 kDa 
• Atom Count: 5,058 
• Modelled Residue Count: 590 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A, B	299	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: envA, lpxC, PA4406 EC: 3.5.1
UniProt
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P47205  Go to UniProtKB:  P47205

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2SZ	D [auth A], F [auth B]	6-(1H-benzimidazol-1-yl)-N-hydroxy-5-[4-({6-[(4-methylpiperazin-1-yl)methyl]pyridin-3-yl}ethynyl)phenyl]pyridine-3-carboxamide C32 H29 N7 O2 YJCPLYNHCKYCMY-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.219 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.77	α = 90
b = 157.115	β = 101.87
c = 48.946	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
PHASES	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Olivier, N.B., Lahiri, S.D., Prince, D.B.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations