8QMB | pdb_00008qmb

Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin

PDB DOI: https://doi.org/10.2210/pdb8QMB/pdb
NAKB: 8QMB

Classification: ISOMERASE
Organism(s): Streptococcus pneumoniae, Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-09-21 Released: 2024-10-02
Deposition Author(s): Najmudin, S., Pan, X.S., Wang, B., Chayen, N.E., Fisher, L.M., Sanderson, M.R.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.206 (Depositor), 0.184 (DCC)
R-Value Work:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of topoisomerase targeting by delafloxacin.

Najmudin, S., Pan, X.S., Wang, B., Govada, L., Chayen, N.E., Rubio, N., Shaffer, M.S.P., Rzepa, H.S., Fisher, L.M., Sanderson, M.R.

(2025) Nat Commun 16: 5829-5829

PubMed: 40595483 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-60688-3
Primary Citation Related Structures:
8C41, 8QMB, 8QMC

PubMed Abstract:
Delafloxacin is a potent anionic fluoroquinolone approved for the treatment of respiratory infections that acts by trapping the DNA cleavage complexes of bacterial topoisomerase IV and gyrase. Its N-1-pyridinyl-, C-7-azetidinyl- and C-8-chlorine substituents confer enhanced antibiotic activity against bacteria resistant to other fluoroquinolones, but its mode of action is unclear. Here we present the X-ray crystal structures of a delafloxacin-DNA cleavage complex obtained by co-crystallization with Streptococcus pneumoniae topo IV using a graphene nucleant and solved at 2.0 and 2.4 Å resolution. The two Mg ²⁺-chelated delafloxacin molecules intercalated at the DNA cleavage site are bound in an unusual conformation involving interacting out-of-plane N-1-aromatic- and C-8-chlorine- substituents. The unprecedented resolution allows comprehensive imaging of water-metal ion links integrating enzyme and DNA through drug-bound and active-site Mg ²⁺ ions plus the discovery of enzyme-bound K ⁺ ions. Our studies on delafloxacin action suggest that intrinsic target affinity contributes to its activity against quinolone-resistant bacteria.

Organizational Affiliation

Molecular and Cellular Sciences Section, Neuroscience and Cell Biology Research Institute, City St George's, University of London, Cranmer Terrace, London, UK.

Macromolecule Content

Total Structure Weight: 181.44 kDa
Atom Count: 13,475
Modeled Residue Count: 1,484
Deposited Residue Count: 1,520
Unique protein chains: 1
Unique nucleic acid chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A	A, B	742	Streptococcus pneumoniae	Mutation(s): 3 Gene Names: parE, SP_0852, parC, SP_0855 EC: 5.6.2.2
UniProt
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P72525 Go to UniProtKB: P72525
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q59961 Go to UniProtKB: Q59961
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q59961 P72525
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(TPGPTPGPGPAPT)-3')	C [auth E]	7	Escherichia coli
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(PGPGPTPTPAPTPCPCPAPCP*A)-3')	D [auth F]	11	Escherichia coli
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
DNA (5'-D(GPTPAPAPTPAPC)-3')	E [auth G]	7	Escherichia coli
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 5
DNA (5'-D(PAPAPCPCPGPTPAPTPTPAP*C)-3')	F [auth H]	11	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TE9 (Subject of Investigation/LOI) Query on TE9 Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth H] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth H] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth H]	BA [auth F], CA [auth H]	delafloxacin C₁₈ H₁₂ Cl F₃ N₄ O₄ DYDCPNMLZGFQTM-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth H] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth H]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Z [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Z [auth B]	K [auth A], L [auth A], Z [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain Z [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain Z [auth B]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A]	M [auth A], O [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain O [auth A] Interactions & Density Focus chain M [auth A] Focus chain O [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Q [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	N [auth A], Q [auth A], W [auth B], X [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain N [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain N [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Y [auth B]	AA [auth B], P [auth A], R [auth A], Y [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain P [auth A] Focus chain R [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain P [auth A] Focus chain R [auth A] Focus chain Y [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain V [auth B] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B] mmCIF format, chain J [auth A] mmCIF format, chain V [auth B]	J [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain V [auth B] Interactions & Density Focus chain J [auth A] Focus chain V [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B]	G [auth A] H [auth A] I [auth A] S [auth B] T [auth B] G [auth A], H [auth A], I [auth A], S [auth B], T [auth B], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]