38LQ | pdb_000038lq

Structure of Staphylococcus aureus Y131F DNA gyrase GK-del fusion construct in complex with 20 bp DNA and OSU-276

PDB DOI: https://doi.org/10.2210/pdb38LQ/pdb

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2026-09-02 Released: 2026-10-21
Deposition Author(s): Tomaszewski, A.J., Bell, C.E.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.238 (Depositor), 0.269 (DCC)
R-Value Work:
0.169 (Depositor), 0.192 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

OSUAB-0276, a Novel Bacterial Topoisomerase Inhibitor (NBTI) with Dual Activity Against Bacterial and Human Type II Topoisomerases

Cassel, S.R., Powell, J.P., Wheat, C.T., Tomaszewski, A.J., Dellos-Nolan, S., Landgraf, A.D., Sham, M.P., Chen, A., Bell, C.E., Wozniak, D.J., Yalowich, J.C., Mitton-Fry, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 169.79 kDa
Atom Count: 12,471
Modeled Residue Count: 1,381
Deposited Residue Count: 1,426
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B,DNA gyrase subunit A	A, B	693	Staphylococcus aureus	Mutation(s): 1 Gene Names: gyrB, SAV0005, gyrA, SA0006 EC: 5.6.2.2
UniProt
Find proteins for P66936 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore P66936 Go to UniProtKB: P66936
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315)) Explore Q99XG5 Go to UniProtKB: Q99XG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P66936 Q99XG5
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(PAPGPCPCPGPTPAPGPGPGPCPCPCPTPAPCPGPGPCPT)-3')	C, D	20	Staphylococcus aureus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1DMB Query on A1DMB Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	(6P)-6-(1-{1-[2-(3-fluoro-6-methoxy-1,5-naphthyridin-4-yl)ethyl]piperidin-4-yl}-1H-1,2,3-triazol-4-yl)-2H-1,4-benzoxazin-3(4H)-one C₂₆ H₂₆ F N₇ O₃ XNAYNSGJXZWWKI-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]