5CDR Isomerase date Jul 04, 2015
title 2.65 Structure Of S.Aureus Dna Gyrase And Artificially Nicke
authors B.D.Bax, V.Srikannathasan, P.F.Chan
compound source
Molecule: Dna Gyrase Subunit A
Chain: A, C
Ec: 5.99.1.3
Engineered: Yes
Mutation: 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,Dna Gyrase Subunit B
Chain: B, D
Ec: 5.99.1.3,5.99.1.3
Engineered: Yes
Mutation: 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(Apgpcpcpgptpap)-3')
Chain: E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpgptpapcpcptpapcpgpgpcpt)
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Apgpcpcpgptpapgpgptpapcpcptpapcpgpgpcp
Chain: F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 61
R_factor 0.188 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.395 93.395 410.583 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.65 Å
ligand GOL, MN enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceStructural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin., Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R, Theobald AJ, Stavenger RA, Bax BD, Gwynn MN, Nat Commun. 2015 Dec 7;6:10048. doi: 10.1038/ncomms10048. PMID:26640131
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (460 Kb) [Save to disk]
  • Biological Unit Coordinates (5cdr.pdb1.gz) 452 Kb
  • LPC: Ligand-Protein Contacts for 5CDR
  • CSU: Contacts of Structural Units for 5CDR
  • Structure Factors (589 Kb)
  • Retrieve 5CDR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CDR from S2C, [Save to disk]
  • Re-refined 5cdr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5CDR 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 5CDR
  • 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: [5cdr_E] [5cdr_B] [5cdr_D] [5cdr_F] [5cdr] [5cdr_C] [5cdr_G] [5cdr_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5CDR: [TOP2c] [TOP4c ] by SMART
    • Other resources with information on 5CDR
  • Community annotation for 5CDR at PDBWiki (http://pdbwiki.org)

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