9NSZ | pdb_00009nsz

OXA-23-NA-1-157, 6 minute soak


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.200 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Dual mechanism of the OXA-23 carbapenemase inhibition by the carbapenem NA-1-157.

Toth, M.Stewart, N.K.Quan, P.Khan, M.M.K.Cox, J.Buynak, J.D.Smith, C.A.Vakulenko, S.B.

(2025) Antimicrob Agents Chemother : e0091825-e0091825

  • DOI: https://doi.org/10.1128/aac.00918-25
  • Primary Citation of Related Structures:  
    9NSW, 9NSX, 9NSY, 9NSZ, 9NT0

  • PubMed Abstract: 

    Carbapenem-resistant Acinetobacter baumannii continues to be a leading cause of life-threatening infections that result in high mortality rates. The major cause of carbapenem resistance in this pathogen is the production of class D carbapenemases, enzymes that inactivate the last resort carbapenem antibiotics, thus significantly diminishing the available therapeutic options. In this study, we evaluated the interaction of OXA-23, the most widely disseminated class D carbapenemase in A. baumannii clinical isolates, with the atypically modified carbapenem, NA-1-157. The MICs of this compound against strains producing OXA-23 were reduced from highly resistant levels observed for the commercial carbapenems meropenem and imipenem (16-128 µg/mL) to sensitive or intermediate levels (2-4 µg/mL). Kinetic studies showed that NA-1-157 inhibits the enzyme due to a significant decrease (>2,000-fold) in the deacylation rate relative to its closest structural analog, meropenem. Structural studies and molecular dynamics simulations demonstrated that inhibition is caused by both the inability of a water molecule to get close enough to the scissile bond to perform deacylation and by partial decarboxylation of the catalytic lysine residue upon formation of the acyl-enzyme intermediate.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase OXA-23273Acinetobacter baumanniiMutation(s): 0 
Gene Names: OXA-23ari-1bla-OXA-23bla_2bla_3blaOXAblaOXA-23ABUW_0563
EC: 3.5.2.6
UniProt
Find proteins for Q9L4P2 (Acinetobacter baumannii)
Explore Q9L4P2 
Go to UniProtKB:  Q9L4P2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L4P2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.771α = 90
b = 82.771β = 90
c = 86.045γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01 AI155723

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Database references