› 7dq0

X-ray diffraction
2Å resolution

Crystal structure of actinomycin D-echinomycin-d(ACGTGCT/AGCTCGT) complex

Released:
DOI: 10.2210/pdb7dq0/pdb
PDB entry 7dq0 coloured by chain, front view.
PDB entry 7dq0 coloured by chain, side view.
PDB entry 7dq0 coloured by chain, top view.
Source organism: Streptomyces sp.
Primary publication:
Synergistic binding of actinomycin D and echinomycin to DNA mismatch sites and their combined anti-tumour effects.
Satange R, Chang CC, Li LY, Lin SH, Neidle S, Hou MH
Nucleic Acids Res (2023)
PMID: 36919604

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-121219 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Actinomycin D Chain: C
Molecule details ›
Chain: C
Length: 11 amino acids
Theoretical weight: 1.26 KDa
Source organism: Streptomyces sp.
Echinomycin Chain: D
Molecule details ›
Chain: D
Length: 8 amino acids
Theoretical weight: 809 Da
Source organism: Streptomyces sp.
DNA (5'-D(P*AP*GP*CP*TP*CP*GP*T)-3') Chain: A
Molecule details ›
Chain: A
Length: 7 nucleotides
Theoretical weight: 2.11 KDa
DNA (5'-D(P*AP*GP*CP*TP*CP*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 7 nucleotides
Theoretical weight: 2.11 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 3 x ZN
Ligand CL 1 x CL
Ligand QUI 2 x QUI
4 modified residues:
Ligand DVA 2 x DVA
Ligand SAR 2 x SAR
Ligand MVA 4 x MVA
Ligand DSN 2 x DSN

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P41212
Unit cell:
a: 30.188Å b: 30.188Å c: 137.608Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.232 0.249

Quick links

Citations

2 mentions without citation

Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism.
Satange et al. (2022)
1 more