5FQ9 | pdb_00005fq9

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.181 (Depositor), 0.192 (DCC)
R-Value Work:
0.157 (Depositor), 0.172 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/ncomms12406
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14489
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C6S Query on C6S Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	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		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	D [auth A], E [auth A], F [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on 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 (Depositor), 0.192 (DCC)
R-Value Work: 0.157 (Depositor), 0.172 (DCC)
R-Value Observed: 0.158 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Revision History (Full details and data files)

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