4S2I

CTX-M-15 in complex with Avibactam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular Mechanism of Avibactam-Mediated beta-Lactamase Inhibition.

King, D.T.King, A.M.Lal, S.M.Wright, G.D.Strynadka, N.C.

(2015) ACS Infect Dis 1: 175-184

  • DOI: 10.1021/acsinfecdis.5b00007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Emerging β-lactamase-mediated resistance is threatening the clinical utility of the single most prominent class of antibacterial agents used in medicine, the β-lactams. The diazabicyclooctane avibactam is able to inhibit a wider range of serine β-lac ...

    Emerging β-lactamase-mediated resistance is threatening the clinical utility of the single most prominent class of antibacterial agents used in medicine, the β-lactams. The diazabicyclooctane avibactam is able to inhibit a wider range of serine β-lactamases than has been previously observed with β-lactamase inhibitors such as the widely prescribed clavulanic acid. However, despite its broad-spectrum activity, variable levels of inhibition have been observed for molecular class D β-lactamases. In order to better understand the molecular basis and spectrum of inhibition by avibactam, we provide structural and mechanistic analysis of the compound in complex with important class A and D serine β-lactamases. Herein, we reveal the 1.7- and 2.0-Å-resolution crystal structures of avibactam covalently bound to class D β-lactamases OXA-10 and OXA-48. Furthermore, a kinetic analysis of key active-site mutants for class A β-lactamase CTX-M-15 allows us to propose a validated mechanism for avibactam-mediated β-lactamase inhibition including a unique role for S130, which acts as a general base. This study provides molecular insights that will aid in the design and development of avibactam-based chemotherapeutic agents effective against emerging drug-resistant microorganisms.


    Organizational Affiliation

    The Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia , 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
263Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaCTX-M-15
EC: 3.5.2.6
Find proteins for G3G192 (Klebsiella pneumoniae)
Go to UniProtKB:  G3G192
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NXL
Query on NXL

Download SDF File 
Download CCD File 
A, B
(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
avibactam, bound form, NXL104, bound form
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.010α = 90.00
b = 60.650β = 104.00
c = 71.500γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MxDCdata collection
PHASERphasing
BUSTERrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Non-polymer description
  • Version 1.2: 2016-09-28
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description