4MSS

Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-acetamido-4,5,6-trihydroxyazepane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selective trihydroxyazepane NagZ inhibitors increase sensitivity of Pseudomonas aeruginosa to beta-lactams.

Mondon, M.Hur, S.Vadlamani, G.Rodrigues, P.Tsybina, P.Oliver, A.Mark, B.L.Vocadlo, D.J.Bleriot, Y.

(2013) Chem.Commun.(Camb.) 49: 10983-10985

  • DOI: 10.1039/c3cc46646a

  • PubMed Abstract: 
  • AmpC β-lactamase confers resistance to β-lactam antibiotics in many Gram negative bacteria. Inducible expression of AmpC requires an N-acetylglucosaminidase termed NagZ. Here we describe the synthesis and characterization of hydroxyazepane inhibitors ...

    AmpC β-lactamase confers resistance to β-lactam antibiotics in many Gram negative bacteria. Inducible expression of AmpC requires an N-acetylglucosaminidase termed NagZ. Here we describe the synthesis and characterization of hydroxyazepane inhibitors of NagZ. We find that these inhibitors enhance the susceptibility of clinically relevant Pseudomonas aeruginosa to β-lactams.


    Organizational Affiliation

    Université de Poitiers, IC2MP, UMR CNRS 7285, Équipe "Synthése Organique" Groupe Glycochimie, 4 rue Michel Brunet, 86022 Poitiers Cedex, France. yves.bleriot@univ-poitiers.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-hexosaminidase 1
A, B
350Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)Mutation(s): 0 
Gene Names: nagZ1 (nagZ, nagZ2)
EC: 3.2.1.52
Find proteins for B4EA43 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Go to UniProtKB:  B4EA43
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2CZ
Query on 2CZ

Download SDF File 
Download CCD File 
A, B
N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]acetamide
C8 H16 N2 O4
RGHXJBVAPJFIEQ-RULNZFCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2CZKi: 3600 nM BINDINGMOAD
2CZKi: 400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.135 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.760α = 90.00
b = 87.580β = 92.10
c = 67.210γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references