8QMC

High resolution structure of the Streptococcus pneumoniae topoisomerase IV-complex with the V-site 18mer dsDNA and novel fluoroquinolone Delafloxacin

PDB DOI: https://doi.org/10.2210/pdb8QMC/pdb
NAKB: 8QMC

Classification: ISOMERASE
Organism(s): Streptococcus pneumoniae, DNA molecule
Expression System: Escherichia coli
Mutation(s): No

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: 2.40 Å
R-Value Free: 0.299
R-Value Work: 0.241

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: 180.91 kDa
Atom Count: 12,797
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 (ATP-hydrolyzing),DNA topoisomerase 4 subunit A	A, B	742	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: AMCSP13_000989, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72525
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(T)-R(PG)-D(PT)-R(PGPGPA)-D(P*T)-3')	C [auth E]	7	DNA molecule
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(PGPG)-D(PTPT)-R(PA)-D(PT)-R(PCPCPAPCP*A)-3')	D [auth F]	11	DNA molecule
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(PAPAPCPCPG)-D(PT)-R(PA)-D(PTPT)-R(PAP*C)-3')	E [auth H]	11	DNA molecule
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(G)-D(PT)-R(PAPA)-D(PT)-R(PAP*C)-3')	F [auth G]	7	DNA molecule
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 T [auth F] SDF format, chain U [auth H] MOL2 format, chain T [auth F] MOL2 format, chain U [auth H] mmCIF format, chain T [auth F] mmCIF format, chain U [auth H]	T [auth F], U [auth H]	delafloxacin C₁₈ H₁₂ Cl F₃ N₄ O₄ DYDCPNMLZGFQTM-UHFFFAOYSA-N		Interactions Focus chain T [auth F] Focus chain U [auth H] Interactions & Density Focus chain T [auth F] Focus chain U [auth H]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain S [auth B] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] mmCIF format, chain N [auth A] mmCIF format, chain S [auth B]	N [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth A] Focus chain S [auth B] Interactions & Density Focus chain N [auth A] Focus chain S [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	K [auth A] L [auth A] M [auth A] P [auth B] Q [auth B] K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]