› 3i1d

X-ray diffraction
2.5Å resolution

Distinct recognition of three-way DNA junctions by the two enantiomers of a metallo-supramolecular cylinder ('helicate')

Released:
DOI: 10.2210/pdb3i1d/pdb
PDB entry 3i1d coloured by chain, front view.
PDB entry 3i1d coloured by chain, side view.
PDB entry 3i1d coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Self-assembly of functionalizable two-component 3D DNA arrays through the induced formation of DNA three-way-junction branch points by supramolecular cylinders.
Boer DR, Kerckhoffs JM, Parajo Y, Pascu M, Usón I, Lincoln P, Hannon MJ, Coll M
Angew Chem Int Ed Engl 49 2336-9 (2010)
PMID: 20191645

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo trimer (preferred)
homo hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-116389 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*CP*GP*TP*AP*CP*G)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand FE2 6 x FE2
Ligand NPM 9 x NPM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4, ESRF BEAMLINE BM16
Spacegroup: P4332
Unit cell:
a: 74.97Å b: 74.97Å c: 74.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.245 0.245 0.259
Expression system: Not provided

Quick links

Citations

3 review citations

DNA-based self-assembly for functional nanomaterials.
Wang et al. (2013)
2 more

3 mentions without citation

Interactions of small molecules with DNA junctions.
McQuaid et al. (2022)
2 more