4HBU | pdb_00004hbu

Crystal structure of CTX-M-15 extended-spectrum beta-lactamase in complex with avibactam (NXL104)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.122 (Depositor), 0.135 (DCC) 
  • R-Value Work: 
    0.104 (Depositor) 
  • R-Value Observed: 
    0.105 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structural insight into potent broad-spectrum inhibition with reversible recyclization mechanism: avibactam in complex with CTX-M-15 and Pseudomonas aeruginosa AmpC beta-lactamases

Lahiri, S.D.Mangani, S.Durand-Reville, T.Benvenuti, M.De Luca, F.Sanyal, G.Docquier, J.D.

(2013) Antimicrob Agents Chemother 57: 2496-2505

  • DOI: https://doi.org/10.1128/AAC.02247-12
  • Primary Citation Related Structures: 
    4GZB, 4HBT, 4HBU, 4HEF

  • PubMed Abstract: 

    Although β-lactams have been the most effective class of antibacterial agents used in clinical practice for the past half century, their effectiveness on Gram-negative bacteria has been eroded due to the emergence and spread of β-lactamase enzymes that are not affected by currently marketed β-lactam/β-lactamase inhibitor combinations. Avibactam is a novel, covalent, non-β-lactam β-lactamase inhibitor presently in clinical development in combination with either ceftaroline or ceftazidime. In vitro studies show that avibactam may restore the broad-spectrum activity of cephalosporins against class A, class C, and some class D β-lactamases. Here we describe the structures of two clinically important β-lactamase enzymes bound to avibactam, the class A CTX-M-15 extended-spectrum β-lactamase and the class C Pseudomonas aeruginosa AmpC β-lactamase, which together provide insight into the binding modes for the respective enzyme classes. The structures reveal similar binding modes in both enzymes and thus provide a rationale for the broad-spectrum inhibitory activity of avibactam. Identification of the key residues surrounding the binding pocket allows for a better understanding of the potency of this scaffold. Finally, avibactam has recently been shown to be a reversible inhibitor, and the structures provide insights into the mechanism of avibactam recyclization. Analysis of the ultra-high-resolution CTX-M-15 structure suggests how the deacylation mechanism favors recyclization over hydrolysis.


  • Organizational Affiliation
    • Infection Biosciences, AstraZeneca R&D Boston, Waltham, Massachusetts, USA.

Macromolecule Content 

  • Total Structure Weight: 29.45 kDa 
  • Atom Count: 2,386 
  • Modeled Residue Count: 261 
  • Deposited Residue Count: 263 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase263Escherichia coliMutation(s): 0 
Gene Names: blaUOE-1blabla CTX-M-15blaCTX-M-15blaCTX-M15CTX-M-15
EC: 3.5.2.6
UniProt
Find proteins for Q9EXV5 (Escherichia coli)
Explore Q9EXV5 
Go to UniProtKB:  Q9EXV5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EXV5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NXL

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
WJDGWXPPFHLLNL-RITPCOANSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
M [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.122 (Depositor), 0.135 (DCC) 
  • R-Value Work:  0.104 (Depositor) 
  • R-Value Observed: 0.105 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.483α = 90
b = 45.686β = 90
c = 117.721γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata 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: 2013-04-10
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Non-polymer description
  • Version 1.3: 2019-12-04
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2024-11-06
    Changes: Structure summary