4KPF Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate date
authors Laponogov, I., Pan, X.S., Vesekov, D.A., Cirz, R.T., Wagman, A.S., Moser, H.E., Fisher, L.M., Sanderson, M.R.
compound source
symmetry
R_factor
R_Free 0.1845
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.24
ligand 1UV, MG enzyme
Gene SP
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceExploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones., Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A, Moser HE, Fisher LM, Sanderson MR, Open Biol. 2016 Sep;6(9). pii: rsob.160157. doi: 10.1098/rsob.160157. PMID:27655731
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (495 Kb) [Save to disk]
  • Biological Unit Coordinates (4kpf.pdb1.gz) 480 Kb
  • LPC: Ligand-Protein Contacts for 4KPF
  • CSU: Contacts of Structural Units for 4KPF
  • Structure Factors (387 Kb)
  • Retrieve 4KPF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KPF from S2C, [Save to disk]
  • Re-refined 4kpf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4KPF 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 4KPF
  • 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
  • 3D motif for 4KPF, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kpf_A] [4kpf_B] [4kpf] [4kpf_F] [4kpf_E] [4kpf_D] [4kpf_C] [4kpf_G] [4kpf_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KPF: [TOP2c] [TOP4c ] by SMART
    • Other resources with information on 4KPF
  • Community annotation for 4KPF at PDBWiki (http://pdbwiki.org)

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