› 4hiv

X-ray diffraction
2.6Å resolution

Structure of actinomycin D d(ATGCGGCAT) complex

Released:
DOI: 10.2210/pdb4hiv/pdb
PDB entry 4hiv coloured by chain, front view.
PDB entry 4hiv coloured by chain, side view.
PDB entry 4hiv coloured by chain, top view.
Source organism: Streptomyces antibioticus
Primary publication:
The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats.
Lo YS, Tseng WH, Chuang CY, Hou MH
Nucleic Acids Res 41 4284-94 (2013)
PMID: 23408860

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-117593 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
ACTINOMYCIN D Chains: C, D
Molecule details ›
Chains: C, D
Length: 11 amino acids
Theoretical weight: 1.26 KDa
Source organism: Streptomyces antibioticus
DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 9 nucleotides
Theoretical weight: 2.76 KDa
Source organism: Streptomyces antibioticus
Expression system: Not provided

Ligands and Environments

No bound ligands
3 modified residues:
Ligand DVA 4 x DVA
Ligand SAR 4 x SAR
Ligand MVA 4 x MVA

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P6522
Unit cell:
a: 86.936Å b: 86.936Å c: 49.778Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.26 0.26 0.29
Expression system: Not provided

Quick links

Citations

3 review citations

Finding needles in a basestack: recognition of mismatched base pairs in DNA by small molecules.
Granzhan et al. (2014)
2 more

4 mentions without citation

A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding.
Satange et al. (2018)
3 more