9H12 | pdb_00009h12

Crystal structure of OXA-48 in complex with nacubactam

PDB DOI: https://doi.org/10.2210/pdb9H12/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-09 Released: 2025-09-03
Deposition Author(s): Hoff, J.F., Goudar, K.E., Hinchliffe, P., Spencer, J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free:
0.192 (Depositor), 0.192 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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 16: 5441-5455

PubMed: 40927637 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d5md00512d
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 60.1 kDa
Atom Count: 4,685
Modeled Residue Count: 490
Deposited Residue Count: 490
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	245	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bla OXA-48, bla_4, blaOXA-48, AI2879V1_5232, GJJ21_26815, KPE71T_00045, SAMEA3727706_05517 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0 Go to UniProtKB: Q6XEC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6XEC0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OP0 (Subject of Investigation/LOI) Query on OP0 Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain EA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain EA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain EA [auth B]	EA [auth B], Q [auth A]	(2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C₉ H₁₈ N₄ O₇ S YTAWXXHGLPATIN-SFYZADRCSA-N		Interactions Focus chain EA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain EA [auth B] Focus chain Q [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain Z [auth B]	Z [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain HA [auth B] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], G [auth A], HA [auth B], U [auth A], V [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain HA [auth B] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain HA [auth B] Focus chain U [auth A] Focus chain V [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain CA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain CA [auth B]	CA [auth B], F [auth A], H [auth A], I [auth A], J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain CA [auth B] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain Y [auth B] SDF format, chain AA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain AA [auth B]	AA [auth B], W [auth A], Y [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain W [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain W [auth A] Focus chain Y [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain R [auth A] SDF format, chain FA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain R [auth A] MOL2 format, chain FA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain R [auth A] mmCIF format, chain FA [auth B]	FA [auth B], R [auth A], T [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain R [auth A] Focus chain T [auth A] Interactions & Density Focus chain FA [auth B] Focus chain R [auth A] Focus chain T [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain S [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain IA [auth B] SDF format, chain GA [auth B] SDF format, chain DA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain S [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain DA [auth B]	BA [auth B] DA [auth B] GA [auth B] IA [auth B] K [auth A] BA [auth B], DA [auth B], GA [auth B], IA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], S [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain DA [auth B] Focus chain GA [auth B] Focus chain IA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth A] Interactions & Density Focus chain BA [auth B] Focus chain DA [auth B] Focus chain GA [auth B] Focus chain IA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain X [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain X [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain X [auth B]