› 2d55

X-ray diffraction
3Å resolution

Structural, physical and biological characteristics of RNA.DNA binding agent N8-actinomycin D

Released:
DOI: 10.2210/pdb2d55/pdb
PDB entry 2d55 coloured by chain, front view.
PDB entry 2d55 coloured by chain, side view.
PDB entry 2d55 coloured by chain, top view.
Source organism: Streptomyces antibioticus
Primary publication:
Crystal structure of the 2:1 complex between d(GAAGCTTC) and the anticancer drug actinomycin D.
Kamitori S, Takusagawa F
J Mol Biol 225 445-56 (1992)
PMID: 1593629

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-115157 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
ACTINOMYCIN D Chain: C
Molecule details ›
Chain: C
Length: 11 amino acids
Theoretical weight: 1.29 KDa
Source organism: Streptomyces antibioticus
DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: Streptomyces antibioticus
Expression system: Not provided

Ligands and Environments

No bound ligands
3 modified residues:
Ligand DVA 2 x DVA
Ligand SAR 2 x SAR
Ligand MVA 2 x MVA

Experiments and Validation Details

Entry percentile scores
Spacegroup: C2
Unit cell:
a: 51.37Å b: 62.09Å c: 25.04Å
α: 90° β: 113.8° γ: 90°
R-values:
R R work R free
0.19 0.19 not available
Expression system: Not provided

Quick links

Citations

7 review citations

Natural product DNA major groove binders.
Hamilton et al. (2012)
6 more

1 mention without citation

A large-scale association study for nanoparticle C60 uncovers mechanisms of nanotoxicity disrupting the native conformations of DNA/RNA.
Xu et al. (2012)