9AZU | pdb_00009azu

Crystal structure of PDC-3 beta-lactamase in complex with taniborbactam

PDB DOI: https://doi.org/10.2210/pdb9AZU/pdb

Classification: HYDROLASE/ANTIBIOTIC
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-11 Released: 2025-03-19
Deposition Author(s): Kumar, V., van den Akker, F.
Funding Organization(s): VenatoRx Pharmaceuticals

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.205 (Depositor), 0.216 (DCC)
R-Value Work:
0.166 (Depositor), 0.178 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanisms of Antibiotic Resistance and Inhibition of PDC-88, a Cefepime-Hydrolyzing R2-loop Deletion Variant of Pseudomonas-derived Cephalosporinase

Mack, A.R., Kumar, V., Bethel, C.R., Taracila, M.A., Miller, B.A., Six, D.A., Uehara, T., Papp-Wallace, K.M., van den Akker, F., Bonomo, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 43.81 kDa
Atom Count: 3,129
Modelled Residue Count: 359
Deposited Residue Count: 397
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	A	397	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: ampC EC: 3.5.2.6
UniProt
Find proteins for Q4H482 (Pseudomonas aeruginosa) Explore Q4H482 Go to UniProtKB: Q4H482
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4H482
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KJK (Subject of Investigation/LOI) Query on KJK 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]	(3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid C₁₉ H₂₈ B N₃ O₅ PFZUWUXKQPRWAL-NOLJZWGESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.205 (Depositor), 0.216 (DCC)
R-Value Work: 0.166 (Depositor), 0.178 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.767	α = 90
b = 70.573	β = 90
c = 105.192	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

van den Akker, F.

Funding Organization	Location	Grant Number
VenatoRx Pharmaceuticals	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-03-19
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.