9H11 | pdb_00009h11

Crystal structure of OXA-48 apoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 
    0.187 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Electrostatic interactions influence diazabicyclooctane inhibitor potency against OXA-48-like beta-lactamases.

Hoff, J.F.Goudar, K.E.Calvopina, K.Beer, M.Hinchliffe, P.Shaw, J.M.Tooke, C.L.Takebayashi, Y.Cadzow, A.F.Harmer, N.J.Mulholland, A.J.Schofield, C.J.Spencer, J.

(2025) RSC Med Chem 

  • DOI: https://doi.org/10.1039/d5md00512d
  • Primary Citation of Related Structures:  
    9H11, 9H12, 9H13, 9H14, 9H15, 9H16, 9H17, 9H18, 9HPV

  • PubMed Abstract: 

    Carbapenemases, β-lactamases hydrolysing carbapenem antibiotics, challenge the treatment of multi-drug resistant bacteria. The OXA-48 carbapenemase is widely disseminated in Enterobacterales , necessitating new treatments for producer strains. Diazabicyclooctane (DBO) inhibitors, including avibactam and nacubactam, act on a wide range of enzymes to overcome β-lactamase-mediated resistance. Here we describe investigations on how avibactam and nacubactam inhibit OXA-48 and two variants, OXA-163 and OXA-405, with deletions in the β5-β6 loop neighbouring the active site that modify activity towards different β-lactam classes. Nacubactam is ∼80-fold less potent than avibactam towards OXA-48, but this difference reduces in OXA-163 and OXA-405. Crystal structures and molecular dynamics simulations reveal electrostatic repulsion between Arg214 on the OXA-48 β5-β6 active-site loop and nacubactam, but not avibactam; effects absent from simulations of OXA-163 and OXA-405, which lack Arg214. Crystallographic and mass spectrometry data demonstrate that all three enzymes support desulfation of the bound DBOs. The results indicate that interactions with Arg214 affect DBO potency, suggesting that sequence variation in OXA-48-like β-lactamases affects reactivity towards inhibitors as well as β-lactam substrates.


  • Organizational Affiliation
    • School of Cellular and Molecular Medicine, University of Bristol Bristol BS8 1TD UK Jim.Spencer@bristol.ac.uk.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
245Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bla OXA-48bla_4blaOXA-48AI2879V1_5232GJJ21_26815KPE71T_00045SAMEA3727706_05517
EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae)
Explore Q6XEC0 
Go to UniProtKB:  Q6XEC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XEC0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free:  0.187 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.513α = 90
b = 123.513β = 90
c = 161.564γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomR102376-101

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references