4S2O

OXA-10 in complex with Avibactam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


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:  
    4S2I, 4S2J, 4S2K, 4S2N, 4S2O, 4S2P

  • 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-lactamases than has been previously observed with β-lactamase inhibitors such as the widely prescribed clavulanic acid ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamase OXA-10A, B246Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaoxa10pse2
EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa)
Explore P14489 
Go to UniProtKB:  P14489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14489
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NXL
Query on NXL

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth B],
H [auth B]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.6α = 90
b = 96.5β = 90
c = 125.7γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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