5CDN: 2.8A structure of etoposide with S.aureus DNA gyrase and DNA

PDB ID: 5CDNDownload
MMDB ID: 241174
PDB Deposition Date: 2015/7/4
Updated in MMDB: 2024/01
Experimental Method:
x-ray diffraction
Resolution: 2.79  Å
Source Organism:
Staphylococcus aureus subsp. aureus N315▼
Similar Structures:
Biological Unit for 5CDN: octameric; determined by author and by software (PISA)
Molecular Components in 5CDN
Label Count Molecule
Proteins (4 molecules)
2
DNA Gyrase Subunit a
Molecule annotation
2
DNA Gyrase Subunit B,dna Gyrase Subunit B
Molecule annotation
Nucleotides(4 molecules)
2
DNA (5'-d(p*gp*ap*gp*cp*gp*tp*ap**gp*gp*cp*cp*gp*tp*ap*cp*gp*cp*tp*c)-3')
Molecule annotation
2
DNA (5'-d(p*gp*ap*gp*cp*gp*tp*ap*c*gp*gp*cp*cp*gp*tp*ap*cp*gp*cp*tp*c)-3')
Molecule annotation
Chemicals and Non-standard biopolymers (9 molecules)
1
1
SULFATE IONSULFATE ION
2
2
MANGANESE (II) IONMANGANESE (II) ION
3
3
GLYCEROLGLYCEROL
4
1
SODIUM IONSODIUM ION
5
2
(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside
* 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