9GEF: Experimental localization of metal-binding sites reveals the role of metal ions in the delafloxacin-stabilized Streptococcus pneumoniae topoisomerase IV DNA cleavage complex

PDB ID: 9GEFDownload
MMDB ID: 253785
PDB Deposition Date: 2024/8/8
Updated in MMDB: 2024/10
Experimental Method:
x-ray diffraction
Resolution: 2.62  Å
Source Organism:
Streptococcus pneumoniae▼
Similar Structures:
Biological Unit for 9GEF: hexameric; determined by author and by software (PISA)
Molecular Components in 9GEF
Label Count Molecule
Proteins (2 molecules)
2
DNA Topoisomerase (Atp-hydrolyzing),dna Topoisomerase 4
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 (21 molecules)
1
4
(4S)-2-METHYL-2,4-PENTANEDIOL(4S)-2-METHYL-2,4-PENTANEDIOL
2
4
MAGNESIUM IONMAGNESIUM ION
3
8
POTASSIUM IONPOTASSIUM ION
4
2
CHLORIDE IONCHLORIDE ION
5
1
ACETATE IONACETATE ION
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