› 8c41

X-ray diffraction
2.39Å resolution

High resolution structure of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin

Released:
DOI: 10.2210/pdb8c41/pdb
Model geometry
Fit model/data
PDB entry 8c41 coloured by chain, front view.
PDB entry 8c41 coloured by chain, side view.
PDB entry 8c41 coloured by chain, top view.
Source organisms:
Entry authors: Najmudin S, Pan XS, Wang B, Chayen NE, Fisher LM, Sanderson MR

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-270324 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
DNA topoisomerase 4 subunit A Chains: A, B
Molecule details ›
Chains: A, B
Length: 742 amino acids
Theoretical weight: 84.21 KDa
Source organism: Streptococcus pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: P72525 (Residues: 1-490; Coverage: 60%)
Gene names: SP_0855, parC
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA (5'-D(*CP*AP*TP*GP*AP*AP*T)-3') Chain: E
Molecule details ›
Chain: E
Length: 7 nucleotides
Theoretical weight: 2.12 KDa
Source organism: DNA molecule
Expression system: Not provided
DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3') Chain: F
DNA (5'-D(*CP*GP*TP*GP*CP*AP*T)-3') Chain: G
DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3') Chain: H

Ligands and Environments

4 bound ligands:
Ligand MPD 3 x MPD
Ligand MG 6 x MG
Ligand CL 2 x CL
Ligand TE9 2 x TE9
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P3121
Unit cell:
a: 157.471Å b: 157.471Å c: 212.339Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.195 0.192 0.243
Expression systems:
  • Escherichia coli
  • Not provided

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