6C9C | pdb_00006c9c

Crystal structure of LpxC from Pseudomonas aeruginosa in complex with racemic ligand PT803

• PDB DOI: https://doi.org/10.2210/pdb6C9C/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Pseudomonas aeruginosa UCBPP-PA14
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-01-26 Released: 2019-03-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of LpxC from Pseudomonas aeruginosa in complex with ligand PT803

Delker, S.L., Mayclin, S.J., Phan, J.N., Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

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: 35.01 kDa 
• Atom Count: 2,550 
• Modeled Residue Count: 291 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-acyl-N-acetylglucosamine deacetylase	A	304	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 1  Gene Names: lpxC, PA14_57260 EC: 3.5.1.108
UniProt
Find proteins for Q02H34 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore Q02H34  Go to UniProtKB:  Q02H34

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EU1	B [auth A]	(2R)-4-[4-{4-[(5-chloro-6-methoxypyridin-3-yl)methoxy]phenyl}-2-oxo-3,6-dihydropyridin-1(2H)-yl]-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide C24 H28 Cl N3 O7 S CDFIGPHKVBKXMP-XMMPIXPASA-N
F64	C [auth A]	(2S)-4-[4-{4-[(5-chloro-6-methoxypyridin-3-yl)methoxy]phenyl}-2-oxo-3,6-dihydropyridin-1(2H)-yl]-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide C24 H28 Cl N3 O7 S CDFIGPHKVBKXMP-DEOSSOPVSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.66	α = 90
b = 79.34	β = 92.01
c = 50.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Other
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description