4WZ5 | pdb_00004wz5

Crystal structure of P. aeruginosa OXA10

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.208 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4WZ5

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

4,5-Disubstituted 6-Aryloxy-1,3-dihydrobenzo[c][1,2]oxaboroles Are Broad-Spectrum Serine beta-Lactamase Inhibitors.

McKinney, D.C., Zhou, F., Eyermann, C.J., Ferguson, A.D., Prince, D.B., Breen, J., Giacobbe, R.A., Lahiri, S., Verheijen, J.C.

(2015) ACS Infect Dis 1: 310-316

  • DOI: https://doi.org/10.1021/acsinfecdis.5b00031
  • Primary Citation Related Structures: 
    4WYY, 4WZ4, 4WZ5

  • PubMed Abstract: 

    Bacterially expressed β-lactamases are rapidly eroding the clinical utility of the important β-lactam class of antibacterials, significantly impairing our ability to fight serious bacterial infections. This paper describes a study of oxaborole-derived β-lactamase inhibitors in which crystal structures and computational modeling aided in the rational design of analogues with improved spectrum of activity against class A, C, and D enzymes. Crystal structures of two of these inhibitors covalently bound to two different serine β-lactamases, class C Pseudomonas aeruginosa AmpC and class D OXA-10, are described herein. Improved physicochemical properties as well as increased activity against an array of β-lactamases resulted in substantial restoration of susceptibility to ceftazidime in Escherichia coli and Klebsiella pneumoniae.

    • Organizational Affiliation: 
    • Infection Innovative Medicines, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham Massachusetts 02451, United States.

Macromolecule Content 

  • Total Structure Weight: 112.94 kDa 
  • Atom Count: 8,380 
  • Modeled Residue Count: 980 
  • Deposited Residue Count: 992 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase OXA-10
A, B
248Pseudomonas aeruginosaMutation(s): 0 
Gene Names: bla, oxa10, pse2
EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa)
Explore P14489 
Go to UniProtKB:  P14489
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14489
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase OXA-10
C, D
248Pseudomonas aeruginosaMutation(s): 0 
Gene Names: bla, oxa10, pse2
EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa)
Explore P14489 
Go to UniProtKB:  P14489
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14489
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3VU

Query on 3VU


Download:Ideal Coordinates CCD File
G [auth A],
K [auth B]		{(3R)-6-[(3-amino-1,2,4-thiadiazol-5-yl)oxy]-1-hydroxy-4,5-dimethyl-1,3-dihydro-2,1-benzoxaborol-3-yl}acetic acid
C13 H14 B N3 O5 S
CXFHZAGALDYYDH-SECBINFHSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
H [auth B]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
S [auth D],
T [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CO2

Query on CO2


Download:Ideal Coordinates CCD File
P [auth C],
U [auth D]		CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.208 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.74α = 90
b = 82.35β = 94.54
c = 102.38γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2016-09-28
    Changes: Database references
  • Version 1.2: 2025-04-02
    Changes: Data collection, Database references, Derived calculations, Structure summary