9NT0 | pdb_00009nt0

OXA-23-meropenem, pH 7.5

• PDB DOI: https://doi.org/10.2210/pdb9NT0/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-17 Released: 2025-08-06 
• Deposition Author(s): Smith, C.A., Toth, M., Stewart, N.K., Vakulenko, S.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

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 69: e0091825-e0091825

• PubMed: 40833279 
• DOI: https://doi.org/10.1128/aac.00918-25
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.
Department of Chemistry, Southern Methodist University, Dallas, Texas, USA.
Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California, USA.
Department of Chemistry, Stanford University, Stanford, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.54 kDa 
• Atom Count: 2,177 
• Modeled Residue Count: 246 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase OXA-23	A	273	Acinetobacter baumannii	Mutation(s): 0  Gene Names: OXA-23, ari-1, bla-OXA-23, bla_2, bla_3, blaOXA, blaOXA-23, ABUW_0563 EC: 3.5.2.6
UniProt
Find proteins for Q9L4P2 (Acinetobacter baumannii) Explore Q9L4P2  Go to UniProtKB:  Q9L4P2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MER (Subject of Investigation/LOI)	B [auth A]	(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid C17 H27 N3 O5 S DYQHXZPAIVAJRU-HTXLXMOSSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.991	α = 90
b = 82.991	β = 90
c = 85.128	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Smith, C.A., Toth, M., Stewart, N.K., Vakulenko, S.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01 AI155723

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release
  
• Version 1.1: 2025-09-03
  Changes: Database references
• Version 1.2: 2025-10-15
  Changes: Database references