3P3E

Crystal Structure of the PSEUDOMONAS AERUGINOSA LpxC/LPC-009 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design.

Lee, C.J.Liang, X.Chen, X.Zeng, D.Joo, S.H.Chung, H.S.Barb, A.W.Swanson, S.M.Nicholas, R.A.Li, Y.Toone, E.J.Raetz, C.R.Zhou, P.

(2011) Chem.Biol. 18: 38-47

  • DOI: 10.1016/j.chembiol.2010.11.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • LpxC is an essential enzyme in the lipid A biosynthetic pathway in gram-negative bacteria. Several promising antimicrobial lead compounds targeting LpxC have been reported, though they typically display a large variation in potency against different ...

    LpxC is an essential enzyme in the lipid A biosynthetic pathway in gram-negative bacteria. Several promising antimicrobial lead compounds targeting LpxC have been reported, though they typically display a large variation in potency against different gram-negative pathogens. We report that inhibitors with a diacetylene scaffold effectively overcome the resistance caused by sequence variation in the LpxC substrate-binding passage. Compound binding is captured in complex with representative LpxC orthologs, and structural analysis reveals large conformational differences that mostly reflect inherent molecular features of distinct LpxC orthologs, whereas ligand-induced structural adaptations occur at a smaller scale. These observations highlight the need for a molecular understanding of inherent structural features and conformational plasticity of LpxC enzymes for optimizing LpxC inhibitors as broad-spectrum antibiotics against gram-negative infections.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
A
299Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 1 
Gene Names: lpxC (envA)
EC: 3.5.1.108
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P47205
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3P3
Query on 3P3

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Download CCD File 
A
N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide
C21 H18 N2 O4
VUYMSCCEGRLBAF-BEFAXECRSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

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Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.637α = 90.00
b = 73.608β = 90.00
c = 88.308γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-10-04 
  • Released Date: 2011-01-05 
  • Deposition Author(s): Lee, C.-J., Zhou, P.

Revision History 

  • Version 1.0: 2011-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description
  • Version 1.3: 2018-01-24
    Type: Structure summary