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Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate

X-ray diffraction
3.24Å resolution
PDB entry 4kpf coloured by chain, front view.
PDB entry 4kpf coloured by chain, side view.
PDB entry 4kpf coloured by chain, top view.
Source organism: Streptococcus pneumoniae TIGR4
Assembly composition:
hetero octamer (preferred)
Entry contents: 2 distinct polypeptide molecules
4 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA topoisomerase 4 and DNA
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Multimeric state: hetero octamer
Accessible surface area: 56604.53 Å2
Buried surface area: 21263.8 Å2
Dissociation area: 1,139.49 Å2
Dissociation energy (ΔGdiss): 20.04 kcal/mol
Dissociation entropy (TΔSdiss): 8.92 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117761

Macromolecules

DNA topoisomerase 4 subunit A
Chains: A, B
Length: 496 amino acids
Theoretical weight: 56.46 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli
UniProt:
  • Canonical: P72525 (Residues: 1-488; Coverage: 59%)
Gene names: SP_0855, parC
Pfam: DNA gyrase/topoisomerase IV, subunit A
InterPro:
DNA topoisomerase 4 subunit A in PDB entry 4kpf, assembly 1, front view.
DNA topoisomerase 4 subunit A in PDB entry 4kpf, assembly 1, side view.
DNA topoisomerase 4 subunit A in PDB entry 4kpf, assembly 1, top view.
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DNA topoisomerase 4 subunit B
Chains: C, D
Length: 268 amino acids
Theoretical weight: 30.42 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59961 (Residues: 404-647; Coverage: 38%)
Gene names: SP_0852, parE
Pfam:
InterPro:
CATH: Rossmann fold
DNA topoisomerase 4 subunit B in PDB entry 4kpf, assembly 1, front view.
DNA topoisomerase 4 subunit B in PDB entry 4kpf, assembly 1, side view.
DNA topoisomerase 4 subunit B in PDB entry 4kpf, assembly 1, top view.
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DNA chain E
Name: E-site1
Representative chains: E
Length: 7 nucleotides
Theoretical weight: 2.12 KDa
E-site1 in PDB entry 4kpf, assembly 1, front view.
E-site1 in PDB entry 4kpf, assembly 1, side view.
E-site1 in PDB entry 4kpf, assembly 1, top view.
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DNA chain F
Name: E-site2
Representative chains: F
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
E-site2 in PDB entry 4kpf, assembly 1, front view.
E-site2 in PDB entry 4kpf, assembly 1, side view.
E-site2 in PDB entry 4kpf, assembly 1, top view.
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DNA chain G
Name: E-site3
Representative chains: G
Length: 7 nucleotides
Theoretical weight: 2.11 KDa
E-site3 in PDB entry 4kpf, assembly 1, front view.
E-site3 in PDB entry 4kpf, assembly 1, side view.
E-site3 in PDB entry 4kpf, assembly 1, top view.
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DNA chain H
Name: E-site4
Representative chains: H
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
E-site4 in PDB entry 4kpf, assembly 1, front view.
E-site4 in PDB entry 4kpf, assembly 1, side view.
E-site4 in PDB entry 4kpf, assembly 1, top view.
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