8CUP

X-ray crystal structure of ADC-33 in complex with sulfonamidoboronic acid 6d

• PDB DOI: https://doi.org/10.2210/pdb8CUP/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.216 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.39 kDa 
• Atom Count: 6,365 
• Modelled Residue Count: 718 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth B], B [auth A]	362	Acinetobacter baumannii	Mutation(s): 0  Gene Names: ampC, BAA1790NC_1053, EP550_05490, EP560_12590, EQH48_05445 EC: 3.5.2.6
UniProt
Find proteins for A7Y407 (Acinetobacter baumannii) Explore A7Y407  Go to UniProtKB:  A7Y407

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OZF (Subject of Investigation/LOI)	C [auth B], D [auth A]	3-[(4S)-4-ethyl-5,7,7-trihydroxy-2,2,7-trioxo-6-oxa-2lambda~6~-thia-3-aza-7lambda~5~-phospha-5-boraheptan-1-yl]benzoic acid C11 H17 B N O9 P S OKRPHJKYNCLTSY-SNVBAGLBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.216 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.29	α = 90
b = 83.82	β = 90
c = 203.38	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-05 
Deposition Author(s): Fernando, M.C., Wallar, B.J., Powers, R.A.

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

Revision History  

• Version 1.0: 2023-04-05
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description