› 5yty

X-ray diffraction
1.58Å resolution

Crystal structure of echinomycin-d(ACGACGT/ACGTCGT) complex

Released:
DOI: 10.2210/pdb5yty/pdb
PDB entry 5yty coloured by chain, front view.
PDB entry 5yty coloured by chain, side view.
PDB entry 5yty coloured by chain, top view.
Source organisms:
Primary publication:
Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex.
Wu PC, Tzeng SL, Chang CK, Kao YF, Waring MJ, Hou MH
OpenAccess logo Nucleic Acids Res 46 7396-7404 (2018)
PMID: 29741655

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-119446 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
echinomycin Chains: D, F
Molecule details ›
Chains: D, F
Length: 8 amino acids
Theoretical weight: 809 Da
Source organism: Streptomyces echinatus
DNA (5'-D(P*AP*CP*GP*AP*CP*GP*T)-3') Chain: A
Molecule details ›
Chain: A
Length: 7 nucleotides
Theoretical weight: 2.12 KDa
Source organism: unidentified
Expression system: Not provided
DNA (5'-D(P*AP*CP*GP*TP*CP*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 7 nucleotides
Theoretical weight: 2.11 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand MN 1 x MN
Ligand QUI 4 x QUI
2 modified residues:
Ligand DSN 4 x DSN
Ligand MVA 4 x MVA

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P3112
Unit cell:
a: 46.362Å b: 46.362Å c: 48.005Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.226 0.222 0.263
Expression system: Not provided

Quick links

Citations

1 review citation

Natural marine products as antiprotozoal agents against amitochondrial parasites.
Estrella-Parra et al. (2022)
10 other articles

3 mentions without citation

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