4KPF 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: Parc55
Chain: A, B
Fragment: Parc55
Engineered: 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: Pare30
Chain: C, D
Fragment: Pare30
Engineered: Yes

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

Molecule: E-Site1
Chain: E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: E-Site2
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: E-Site3
Chain: G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: E-Site4
Chain: H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 31 2 1
R_factor 0.162 R_Free 0.185
crystal
cell
length a length b length c angle alpha angle beta angle gamma
157.860 157.860 210.780 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.24 Å
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
  • 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 4KPF, from MSDmotif at EBI
  • Fold representative 4kpf from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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