8QMB: Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin

PDB ID: 8QMBDownload
MMDB ID: 252918
PDB Deposition Date: 2023/9/21
Updated in MMDB: 2024/10
Experimental Method:
x-ray diffraction
Resolution: 2  Å
Source Organism:
Streptococcus pneumoniae▼
Similar Structures:
Biological Unit for 8QMB: hexameric; determined by author and by software (PISA)
Molecular Components in 8QMB
Label Count Molecule
Proteins (2 molecules)
2
DNA Topoisomerase 4 Subunit B,dna Topoisomerase 4 Subunit a
Molecule annotation
Nucleotides(4 molecules)
1
DNA (5'-d(tp*gp*tp*gp*gp*ap*t)-3')
Molecule annotation
1
DNA (5'-d(p*gp*gp*tp*tp*ap*tp*cp*cp*ap*cp*a)-3')
Molecule annotation
1
DNA (5'-d(gp*tp*ap*ap*tp*ap*c)-3')
Molecule annotation
1
DNA (5'-d(p*ap*ap*cp*cp*gp*tp*ap*tp*tp*ap*c)-3')
Molecule annotation
Chemicals and Non-standard biopolymers (23 molecules)
1
6
MAGNESIUM IONMAGNESIUM ION
2
2
CHLORIDE IONCHLORIDE ION
3
3
(4S)-2-METHYL-2,4-PENTANEDIOL(4S)-2-METHYL-2,4-PENTANEDIOL
4
2
MALONIC ACIDMALONIC ACID
5
4
ACETATE IONACETATE ION
6
4
FORMIC ACIDFORMIC ACID
7
2
delafloxacindelafloxacin
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303