› 3d1f

X-ray diffraction
2Å resolution

Crystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide

Released:
DOI: 10.2210/pdb3d1f/pdb
PDB entry 3d1f coloured by chain, front view.
PDB entry 3d1f coloured by chain, side view.
PDB entry 3d1f coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.
Georgescu RE, Yurieva O, Kim SS, Kuriyan J, Kong XP, O'Donnell M
Proc Natl Acad Sci U S A 105 11116-21 (2008)
PMID: 18678908

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141826 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Beta sliding clamp Chains: A, B
Molecule details ›
Chains: A, B
Length: 366 amino acids
Theoretical weight: 40.63 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A988 (Residues: 1-366; Coverage: 100%)
Gene names: JW3678, b3701, dnaN
Sequence domains:
Structure domains: DNA Polymerase III, subunit A, domain 2
Nonapeptide from polymerase III C-terminal Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 9 amino acids
Theoretical weight: 1.1 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand PEG 2 x PEG
Ligand 323 2 x 323
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P32
Unit cell:
a: 65.778Å b: 65.778Å c: 209.472Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.217 0.217 0.255
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

17 review citations

DNA replicases from a bacterial perspective.
McHenry CS. (2011)
16 more

11 mentions without citation

The design and development of covalent protein-protein interaction inhibitors for cancer treatment.
Cheng et al. (2020)
10 more