8CUL

Xray ray crystal structure of OXA-24/40 in complex with CR167

PDB DOI: https://doi.org/10.2210/pdb8CUL/pdb

Classification: Hydrolase/Inhibitor
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-17 Released: 2023-04-05
Deposition Author(s): Fernando, M.C., Wallar, B.J., Powers, R.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.255
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat Resistance in Acinetobacter baumannii

Introvigne, L.M., Beardsley, T.J., Fernando, M.C., Leonard, D.A., Wallar, B.J., Rudin, S.D., Taracila, M.A., Rather, P.N., Colquhoun, J.M., Song, S., Fini, F., Hujer, K.M., Hujer, A.M., Prati, F., Powers, R.A., Bonomo, R.A., Caselli, E.

(2023) Antibiotics (Basel) 12: 644

DOI: https://doi.org/10.3390/antibiotics12040644

Macromolecule Content

Total Structure Weight: 27.99 kDa
Atom Count: 2,070
Modelled Residue Count: 244
Deposited Residue Count: 245
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	245	Acinetobacter baumannii	Mutation(s): 0 Gene Names: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40, SI89_16690 EC: 3.5.2.6
UniProt
Find proteins for Q8RLA6 (Acinetobacter baumannii) Explore Q8RLA6 Go to UniProtKB: Q8RLA6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RLA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0N3 (Subject of Investigation/LOI) Query on 0N3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	3-({[(dihydroxyboranyl)methyl]sulfamoyl}methyl)benzoic acid C₉ H₁₂ B N O₆ S AHCSCYIPIIBZTG-UHFFFAOYSA-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: 2.01 Å
R-Value Free: 0.255
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.585	α = 90
b = 102.585	β = 90
c = 86.174	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI072219

Revision History (Full details and data files)

Version 1.0: 2023-04-05
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.