Structure of the monofunctional Staphylococcus aureus PBP1 in its beta-lactam (Cephalexin) inhibited form

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1.

Bon, C.G.Grigg, J.C.Lee, J.Robb, C.S.Caveney, N.A.Eltis, L.D.Strynadka, N.C.J.

(2024) J Struct Biol 216: 108086-108086

  • DOI: https://doi.org/10.1016/j.jsb.2024.108086
  • Primary Citation of Related Structures:  
    8VBT, 8VBU, 8VBV, 8VBW

  • PubMed Abstract: 

    Staphylococcus aureus, an ESKAPE pathogen, is a major clinical concern due to its pathogenicity and manifold antimicrobial resistance mechanisms. The commonly used β-lactam antibiotics target bacterial penicillin-binding proteins (PBPs) and inhibit crosslinking of peptidoglycan strands that comprise the bacterial cell wall mesh, initiating a cascade of effects leading to bacterial cell death. S. aureus PBP1 is involved in synthesis of the bacterial cell wall during division and its presence is essential for survival of both antibiotic susceptible and resistant S. aureus strains. Here, we present X-ray crystallographic data for S. aureus PBP1 in its apo form as well as acyl-enzyme structures with distinct classes of β-lactam antibiotics representing the penicillins, carbapenems, and cephalosporins, respectively: oxacillin, ertapenem and cephalexin. Our structural data suggest that the PBP1 active site is readily accessible for substrate, with little conformational change in key structural elements required for its covalent acylation of β-lactam inhibitors. Stopped-flow kinetic analysis and gel-based competition assays support the structural observations, with even the weakest performing β-lactams still having comparatively high acylation rates and affinities for PBP1. Our structural and kinetic analysis sheds insight into the ligand-PBP interactions that drive antibiotic efficacy against these historically useful antimicrobial targets and expands on current knowledge for future drug design and treatment of S. aureus infections.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 1
A, B
595Staphylococcaceae bacteriumMutation(s): 0 
Gene Names: SAOUHSC_01145
Find proteins for Q2FZ94 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FZ94 
Go to UniProtKB:  Q2FZ94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FZ94
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
63U (Subject of Investigation/LOI)
Query on 63U

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
C16 H19 N3 O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.076α = 90
b = 72.531β = 103.85
c = 89.595γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release