5FQ9

Crystal structure of the OXA10 with 1C

• PDB DOI: https://doi.org/10.2210/pdb5FQ9/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-08 Released: 2016-08-17 
• Deposition Author(s): Brem, J., McDonough, M.A., Cain, R., Clifton, I., Fishwick, C.W.G., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.181 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates.

Brem, J., Cain, R., Cahill, S., McDonough, M.A., Clifton, I.J., Jimenez-Castellanos, J.C., Avison, M.B., Spencer, J., Fishwick, C.W., Schofield, C.J.

(2016) Nat Commun 7: 12406-12406

• PubMed: 27499424 
• DOI: https://doi.org/10.1038/ncomms12406
• Primary Citation of Related Structures:  
  5FQ9, 5FQB, 5FQC, 5J8X


• PubMed Abstract: 
  

  β-Lactamases enable resistance to almost all β-lactam antibiotics. Pioneering work revealed that acyclic boronic acids can act as 'transition state analogue' inhibitors of nucleophilic serine enzymes, including serine-β-lactamases. Here we report biochemical and biophysical analyses revealing that cyclic boronates potently inhibit both nucleophilic serine and zinc-dependent β-lactamases by a mechanism involving mimicking of the common tetrahedral intermediate. Cyclic boronates also potently inhibit the non-essential penicillin-binding protein PBP 5 by the same mechanism of action. The results open the way for development of dual action inhibitors effective against both serine- and metallo-β-lactamases, and which could also have antimicrobial activity through inhibition of PBPs.

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Organizational Affiliation: 

Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.63 kDa 
• Atom Count: 4,486 
• Modelled Residue Count: 493 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE OXA-10	A, B	248	Pseudomonas aeruginosa	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa) Explore P14489  Go to UniProtKB:  P14489

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C6S	C [auth A], I [auth B]	(3R)-3-(cyclohexylcarbonylamino)-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid C16 H20 B N O5 ZRHUJXRVIMMHFG-ZDUSSCGKSA-N
GOL	D [auth A], E [auth A], F [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.181 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.898	α = 90
b = 103.109	β = 90
c = 125.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Brem, J., McDonough, M.A., Cain, R., Clifton, I., Fishwick, C.W.G., Schofield, C.J.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2018-02-21
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description