5CDP 2.45A structure of etoposide with S.aureus DNA gyrase and DNA date
authors Bax, B.D., Srikannathasan, V., Chan, P.F.
compound source
R_Free 0.2110
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.45
ligand EVP, MN, NA enzyme
A, C

D, B

Primary referenceCrystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide., Srikannathasan V, Wohlkonig A, Shillings A, Singh O, Chan PF, Huang J, Gwynn MN, Fosberry AP, Homes P, Hibbs M, Theobald AJ, Spitzfaden C, Bax BD, Acta Crystallogr F Struct Biol Commun. 2015 Oct 1;71(Pt 10):1242-6. doi:, 10.1107/S2053230X15015290. Epub 2015 Sep 23. PMID:26457513
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (477 Kb) [Save to disk]
  • Biological Unit Coordinates (5cdp.pdb1.gz) 468 Kb
  • LPC: Ligand-Protein Contacts for 5CDP
  • CSU: Contacts of Structural Units for 5CDP
  • Structure Factors (809 Kb)
  • Retrieve 5CDP in mmCIF format [Save to disk]
  • Re-refined 5cdp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CDP in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5CDP
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5cdp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cdp_C] [5cdp_D] [5cdp_G] [5cdp_B] [5cdp] [5cdp_H] [5cdp_A] [5cdp_F] [5cdp_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5CDP: [TOP2c] [TOP4c ] by SMART
  • Other resources with information on 5CDP
  • Community annotation for 5CDP at PDBWiki (http://pdbwiki.org)

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