8QMB

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

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
R-Value Work: 0.169

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The nature of the molecular interactions at high resolution of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin.

Najmudin, S., Pan, X.S., Wang, B., Chayen, N.E., Fisher, L.M., Sanderson, M.R.

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 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 Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q59961 Go to UniProtKB: Q59961
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P72525 Go to UniProtKB: P72525
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q59961P72525
Sequence Annotations Expand
Reference Sequence

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

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

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

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
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]	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]
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]	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]
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]	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]
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]	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]
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]	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]
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]	J [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions 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 T [auth B] SDF format, chain U [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 T [auth B] MOL2 format, chain U [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]