3P3C

Crystal Structure of the Aquifex aeolicus LpxC/LPC-009 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.152 

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:  3P3E, 3P3G

  • 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
274Aquifex aeolicus (strain VF5)Gene Names: lpxC (envA)
EC: 3.5.1.-
Find proteins for O67648 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67648
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3P3
Query on 3P3

Download SDF File 
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
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3P3Kd: 8 nM (99) BINDINGDB
3P3Ki: 1 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.152 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 65.604α = 90.00
b = 65.604β = 90.00
c = 132.263γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

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