› 3oz3

X-ray diffraction
1.57Å resolution

Vinyl Carbocyclic LNA

Released:
DOI: 10.2210/pdb3oz3/pdb
PDB entry 3oz3 coloured by chain, front view.
PDB entry 3oz3 coloured by chain, side view.
PDB entry 3oz3 coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA.
Seth PP, Allerson CR, Berdeja A, Siwkowski A, Pallan PS, Gaus H, Prakash TP, Watt AT, Egli M, Swayze EE
J Am Chem Soc 132 14942-50 (2010)
PMID: 20886816

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116689 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*GP*CP*GP*TP*AP*(UVX)P*AP*CP*GP*C)-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 10 nucleotides
Theoretical weight: 3.07 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MPD 1 x MPD
1 modified residue:
Ligand UVX 2 x UVX

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P212121
Unit cell:
a: 24.419Å b: 44.105Å c: 45.842Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.163 0.208
Expression system: Not provided

Quick links

Citations

6 review citations

Designing chemically modified oligonucleotides for targeted gene silencing.
Deleavey et al. (2012)
5 more