› 3qsb

X-ray diffraction
1.9Å resolution

Structure of E. coli polIIIbeta with (Z)-5-(1-((4'-Fluorobiphenyl-4-yl)methoxyimino)butyl)-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile

Released:
DOI: 10.2210/pdb3qsb/pdb
PDB entry 3qsb coloured by chain, front view.
PDB entry 3qsb coloured by chain, side view.
PDB entry 3qsb coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Binding inhibitors of the bacterial sliding clamp by design.
Wijffels G, Johnson WM, Oakley AJ, Turner K, Epa VC, Briscoe SJ, Polley M, Liepa AJ, Hofmann A, Buchardt J, Christensen C, Prosselkov P, Dalrymple BP, Alewood PF, Jennings PA, Dixon NE, Winkler DA
J Med Chem 54 4831-8 (2011)
PMID: 21604761

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141820 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Beta sliding clamp Chain: A
Molecule details ›
Chain: A
Length: 366 amino acids
Theoretical weight: 40.63 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A988 (Residues: 1-366; Coverage: 100%)
Gene names: JW3678, b3701, dnaN
Sequence domains:
Structure domains: DNA Polymerase III, subunit A, domain 2
Beta sliding clamp Chain: B
Molecule details ›
Chain: B
Length: 366 amino acids
Theoretical weight: 40.65 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A988 (Residues: 1-366; Coverage: 100%)
Gene names: JW3678, b3701, dnaN
Sequence domains:
Structure domains: DNA Polymerase III, subunit A, domain 2

Ligands and Environments

1 bound ligand:
Ligand 743 2 x 743
1 modified residue:
Ligand CSO 1 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21
Unit cell:
a: 79.176Å b: 66.519Å c: 83.117Å
α: 90° β: 115.86° γ: 90°
R-values:
R R work R free
0.246 0.242 0.317
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Replicative DNA polymerases.
Johansson et al. (2013)
4 more

1 mention without citation

Modulators of protein-protein interactions as antimicrobial agents.
Kahan et al. (2021)