4KPE Isomerase Dna Inhibitor date May 13, 2013
title Novel Fluoroquinolones In Complex With Topoisomerase Iv From Pneumoniae And E-Site G-Gate
authors I.Laponogov, X.S.Pan, D.A.Vesekov, R.T.Cirz, A.S.Wagman, H.E.Mos L.M.Fisher, M.R.Sanderson
compound source
Molecule: Dna Topoisomerase 4 Subunit A
Chain: A, B
Fragment: Parc55, Unp Residues 1-488
Synonym: Topoisomerase Iv Subunit A
Ec: 5.99.1.3
Engineered: Yes
Mutation: Yes
Organism_scientific: Streptococcus Pneumoniae
Organism_taxid: 170187
Strain: Atcc Baa-334 Tigr4
Gene: Parc, Sp_0855
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Topoisomerase 4 Subunit B
Chain: C, D
Fragment: Pare30, Unp Residues 404-647
Ec: 5.99.1.3
Engineered: Yes
Mutation: Yes

Organism_scientific: Streptococcus Pneumoniae Serotype 4
Organism_taxid: 170187
Strain: Atcc Baa-334 Tigr4
Gene: Pare
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: E-Site Dna1
Chain: E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: E-Site Dna2
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: E-Site Dna3
Chain: G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: E-Site Dna4
Chain: H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 31 2 1
R_factor 0.154 R_Free 0.195
crystal
cell
length a length b length c angle alpha angle beta angle gamma
157.830 157.830 210.710 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.43 Å
ligand AF5, MG enzyme Isomerase E.C.5.99.1.3 BRENDA
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] (487 Kb) [Save to disk]
  • Biological Unit Coordinates (4kpe.pdb1.gz) 472 Kb
  • LPC: Ligand-Protein Contacts for 4KPE
  • CSU: Contacts of Structural Units for 4KPE
  • Structure Factors (331 Kb)
  • Retrieve 4KPE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KPE from S2C, [Save to disk]
  • Re-refined 4kpe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KPE 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 4KPE
  • 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
  • 3D motif for 4KPE, from MSDmotif at EBI
  • Fold representative 4kpe from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kpe_D] [4kpe_F] [4kpe_E] [4kpe_C] [4kpe_B] [4kpe_H] [4kpe_A] [4kpe] [4kpe_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KPE: [TOP2c] [TOP4c ] by SMART
  • Other resources with information on 4KPE
  • Community annotation for 4KPE at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science