› 5ytz

X-ray diffraction
1.55Å resolution

Crystal structure of echinomycin-d(ACGTCGT)2 complex

Released:
DOI: 10.2210/pdb5ytz/pdb
PDB entry 5ytz coloured by chain, front view.
PDB entry 5ytz coloured by chain, side view.
PDB entry 5ytz 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
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-119447 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 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*TP*CP*GP*(UD))-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 7 nucleotides
Theoretical weight: 2.18 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE TPS 05A
Spacegroup: I4122
Unit cell:
a: 41.759Å b: 41.759Å c: 138.415Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.206 0.235
Expression system: Not provided

Quick links

Citations

8 citation in other articles

Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation.
Satange et al. (2019)
7 more

5 mentions without citation

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