5CDP Isomerase date Jul 04, 2015
title 2.45a Structure Of Etoposide With S.Aureus Dna Gyrase And Dn
authors B.D.Bax, V.Srikannathasan, P.F.Chan
compound source
Molecule: Dna Gyrase Subunit A
Chain: A, C
Fragment: Unp Residues 9-491
Ec: 5.99.1.3
Engineered: Yes
 Organism_scientific: Staphylococcus Aureus (Strain N315)
Organism_taxid: 158879
Strain: N315
Gene: Gyra, Sa0006
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Gyrase Subunit B
Chain: B, D
Fragment: Unp Residues 417-542, 580-640
Synonym: Greek Key Deletion Construct
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes
Organism_scientific: Staphylococcus Aureus (Strain N315)
Organism_taxid: 158879
Strain: N315
Gene: Gyrb, Sa0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Apgpcpcpgptpapggpgptpapcpcptpapcpgpgp
Chain: E, F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Apgpcpcpgptpapggpgptpapcpcptpapcpgpgp
Chain: G, H
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 61
R_factor 0.177 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.364 93.364 411.244 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.45 Å
ligand EVP, MN, NA enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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] (465 Kb) [Save to disk]
  • Biological Unit Coordinates (5cdp.pdb1.gz) 457 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]
  • SEQRES to COORDINATES correlation for 5CDP from S2C, [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
  • 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
    • 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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