9ZOT | pdb_00009zot

OXA-23-JDB/PQ-1-219, 30 min complex

PDB DOI: https://doi.org/10.2210/pdb9ZOT/pdb

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

Deposited: 2025-12-16 Released: 2026-01-14
Deposition Author(s): Smith, C.A., Maggiolo, A.M., Vakulenko, S.B., Toth, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.198 (Depositor), 0.198 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Potent Inhibition of OXA-23 and Unimpeded Access to PBPs Underpins the Broad Activity of the Novel Carbapenem JDB/PQ-1-219 Against Class D Carbapenemases

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

To be published.

Macromolecule Content

Total Structure Weight: 31.44 kDa
Atom Count: 2,121
Modeled Residue Count: 247
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9L4P2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C3I (Subject of Investigation/LOI) Query on A1C3I Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-{[(3S)-2,3-dihydroazet-3-yl]sulfanyl}-2-methyl-2H-pyrrole-5-carboxylic acid C₁₃ H₁₆ N₂ O₅ S BNQPVMFRHIJZIS-IOALNURASA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.198 (Depositor), 0.198 (DCC)
R-Value Work: 0.177 (Depositor), 0.178 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.808	α = 90
b = 82.808	β = 90
c = 86.291	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-14

Deposition Author(s):

Vakulenko, S.B.

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

Revision History (Full details and data files)

Version 1.0: 2026-01-14
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.