4DKI

Structural Insights into the Anti- Methicillin-Resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

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Literature

Structural Insights into the Anti-methicillin-resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole.

Lovering, A.L., Gretes, M.C., Safadi, S.S., Danel, F., de Castro, L., Page, M.G., Strynadka, N.C.

(2012) J Biol Chem 287: 32096-32102

  • DOI: https://doi.org/10.1074/jbc.M112.355644
  • Primary Citation of Related Structures:  
    4DKI

  • PubMed Abstract: 

    Methicillin-resistant Staphylococcus aureus (MRSA) is an antibiotic-resistant strain of S. aureus afflicting hospitals and communities worldwide. Of greatest concern is its development of resistance to current last-line-of-defense antibiotics; new therapeutics are urgently needed to combat this pathogen. Ceftobiprole is a recently developed, latest generation cephalosporin and has been the first to show activity against MRSA by inhibiting essential peptidoglycan transpeptidases, including the β-lactam resistance determinant PBP2a, from MRSA. Here we present the structure of the complex of ceftobiprole bound to PBP2a. This structure provides the first look at the molecular details of an effective β-lactam-resistant PBP interaction, leading to new insights into the mechanism of ceftobiprole efficacy against MRSA.

    • Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 2'
A, B
646Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: mecA, SACOL0033
EC: 3.4.16.4
UniProt
Find proteins for A0A0H2WXF8 (Staphylococcus aureus (strain COL))
Explore A0A0H2WXF8 
Go to UniProtKB:  A0A0H2WXF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2WXF8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RB6
Query on RB6
Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]		(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
C20 H24 N8 O6 S2
MYAXGJQBOYOEHQ-SWBIIUODSA-N
CD
Query on CD
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
N [auth B]
O [auth B]
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
BCT
Query on BCT
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
M [auth B]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CL
Query on CL
Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
R [auth B],
S [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.847α = 90
b = 103.471β = 90
c = 186.5γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary