CDD-1 beta-lactamase in imidazole/MPD 60 minute avibactam complex

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D beta-lactamases.

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

(2021) ACS Infect Dis 7: 1765-1776

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00094
  • Primary Citation of Related Structures:  
    7LNO, 7LNQ, 7LNR, 7ME9, 7MEA, 7MEB, 7MEC, 7MED, 7MEE, 7MEF, 7MEG, 7MEH

  • PubMed Abstract: 

    Class D β-lactamases have risen to notoriety due to their wide spread in bacterial pathogens, propensity to inactivate clinically important β-lactam antibiotics, and ability to withstand inhibition by the majority of classical β-lactamase inhibitors. Understanding the catalytic mechanism of these enzymes is thus vitally important for the development of novel antibiotics and inhibitors active against infections caused by antibiotic-resistant bacteria. Here we report an in crystallo time-resolved study of the interaction of the class D β-lactamase CDD-1 from Clostridioides difficile with the diazobicyclooctane inhibitor, avibactam. We show that the catalytic carboxylated lysine, a residue that is essential for both acylation and deacylation of β-lactams, is sequestered within an internal sealed pocket of the enzyme. Time-resolved snapshots generated in this study allowed us to observe decarboxylation of the lysine and movement of CO 2 and water molecules through a transient channel formed between the lysine pocket and the substrate binding site facilitated by rotation of the side chain of a conserved leucine residue. These studies provide novel insights on avibactam binding to CDD-1 and into the catalytic mechanism of class D β-lactamases in general.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase250Clostridioides difficileMutation(s): 2 
Gene Names: blaR1_1E5F32_07085E5F39_11445SAMEA3374989_01677
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NXL (Subject of Investigation/LOI)
Query on NXL

Download Ideal Coordinates CCD File 
B [auth A](2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C7 H13 N3 O6 S
Query on MPD

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F [auth A],
G [auth A]
C6 H14 O2
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
O4 S
Query on IMD

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
C3 H5 N2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.673α = 90
b = 123.673β = 90
c = 123.673γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release