8QMC: High resolution structure of the Streptococcus pneumoniae topoisomerase IV-complex with the V-site 18mer dsDNA and novel fluoroquinolone Delafloxacin

PDB ID: 8QMCDownload
MMDB ID: 252919
PDB Deposition Date: 2023/9/21
Updated in MMDB: 2024/10
Experimental Method:
x-ray diffraction
Resolution: 2.402  Å
Source Organism:
DNA molecule▼
Similar Structures:
Biological Unit for 8QMC: hexameric; determined by author
Molecular Components in 8QMC
Label Count Molecule
Proteins (2 molecules)
2
DNA Topoisomerase (Atp-hydrolyzing),dna Topoisomerase 4 Subunit a
Molecule annotation
Nucleotides(4 molecules)
1
DNA (5'-d(*t)-r(p*g)-d(p*t)-r(p*gp*gp*a)-d(p*t)-3')
Molecule annotation
1
Dna/rna (5'-r(p*gp*g)-d(p*tp*t)-r(p*a)-d(p*t)-r(p*cp*cp*ap*cp*a)-3')
Molecule annotation
1
Dna/rna (5'-r(p*ap*ap*cp*cp*g)-d(p*t)-r(p*a)-d(p*tp*t)-r(p*ap*c)-3')
Molecule annotation
1
Dna/rna (5'-r(*g)-d(p*t)-r(p*ap*a)-d(p*t)-r(p*ap*c)-3')
Molecule annotation
Chemicals and Non-standard biopolymers (15 molecules)
1
2
MALONIC ACIDMALONIC ACID
2
2
ACETATE IONACETATE ION
3
6
MAGNESIUM IONMAGNESIUM ION
4
2
CHLORIDE IONCHLORIDE ION
5
1
(4S)-2-METHYL-2,4-PENTANEDIOL(4S)-2-METHYL-2,4-PENTANEDIOL
6
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