› 6l01

X-ray diffraction
2.6Å resolution

Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative

Released:
DOI: 10.2210/pdb6l01/pdb
Model geometry
Fit model/data
PDB entry 6l01 coloured by chain, front view.
PDB entry 6l01 coloured by chain, side view.
PDB entry 6l01 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation.
Ushiyama F, Amada H, Takeuchi T, Tanaka-Yamamoto N, Kanazawa H, Nakano K, Mima M, Masuko A, Takata I, Hitaka K, Iwamoto K, Sugiyama H, Ohtake N
OpenAccess logo ACS Omega 5 10145-10159 (2020)
PMID: 32391502

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142496 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA gyrase subunit B Chain: A
Molecule details ›
Chain: A
Length: 220 amino acids
Theoretical weight: 24.19 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AES6 (Residues: 1-220; Coverage: 27%)
Gene names: JW5625, acrB, b3699, cou, gyrB, himB, hisU, nalC, parA, pcbA
Sequence domains: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

Ligands and Environments

1 bound ligand:
Ligand E0U 1 x E0U
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 41.582Å b: 67.066Å c: 68.252Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.23 0.287
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Fragment-to-Lead Medicinal Chemistry Publications in 2020.
de Esch et al. (2022)
1 more

2 mentions without citation

Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation.
Ushiyama et al. (2020)
1 more