7KEQ | pdb_00007keq

avibactam-CDD-1 6 minute complex

• PDB DOI: https://doi.org/10.2210/pdb7KEQ/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-10-11 Released: 2021-01-20 
• Deposition Author(s): Smith, C.A., Vakulenko, S.B., Stewart, N.K., Toth, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.217 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Inhibition of the Clostridioides difficile Class D beta-Lactamase CDD-1 by Avibactam.

Stewart, N.K., Toth, M., Stasyuk, A., Lee, M., Smith, C.A., Vakulenko, S.B.

(2021) ACS Infect Dis 7: 1164-1176

• PubMed: 33390002 
• DOI: https://doi.org/10.1021/acsinfecdis.0c00714
• Primary Citation Related Structures: 
  7KEP, 7KEQ, 7KER


• PubMed Abstract: 
  

  Avibactam is a potent diazobicyclooctane inhibitor of class A and C β-lactamases. The inhibitor also exhibits variable activity against some class D enzymes from Gram-negative bacteria; however, its interaction with recently discovered class D β-lactamases from Gram-positive bacteria has not been studied. Here, we describe microbiological, kinetic, and mass spectrometry studies of the interaction of avibactam with CDD-1, a class D β-lactamase from the clinically important pathogen Clostridioides difficile , and show that avibactam is a potent irreversible mechanism-based inhibitor of the enzyme. X-ray crystallographic studies at three time-points demonstrate the rapid formation of a stable CDD-1-avibactam acyl-enzyme complex and highlight differences in the anchoring of the inhibitor by class D enzymes from Gram-positive and Gram-negative bacteria.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.
Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California 94025, United States.
Department of Chemistry, Stanford University, Stanford, California 94305, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.17 kDa 
• Atom Count: 2,287 
• Modeled Residue Count: 251 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	312	Clostridioides difficile	Mutation(s): 2  Gene Names: blaR1_4, blaR1_1, E5F39_11445, SAMEA2239407_03320, SAMEA3374989_01677 EC: 3.5.2.6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NXL (Subject of Investigation/LOI)	B [auth A]	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C7 H13 N3 O6 S WJDGWXPPFHLLNL-RITPCOANSA-N
FYG	C [auth A]	(2S,5R)-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]octane-2-carboxamide C7 H11 N3 O6 S NDCUAPJVLWFHHB-UHNVWZDZSA-N
MPD	I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.217 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.536	α = 90
b = 123.536	β = 90
c = 123.536	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Smith, C.A., Vakulenko, S.B., Stewart, N.K., Toth, M.

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-05-26
  Changes: Database references
• Version 1.2: 2025-04-02
  Changes: Data collection, Database references, Structure summary