› 3ltu

X-ray diffraction
1.4Å resolution

5-SeMe-dU containing DNA 8mer

Released:
DOI: 10.2210/pdb3ltu/pdb
PDB entry 3ltu coloured by chain, front view.
PDB entry 3ltu coloured by chain, side view.
PDB entry 3ltu coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate
Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z
Chemistryselect 8 (2023)

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-116537 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*GP*(UMS)P*GP*(T5S)P*AP*CP*AP*C)-3' Chain: A
Molecule details ›
Chain: A
Length: 8 nucleotides
Theoretical weight: 2.58 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
2 modified residues:
Ligand UMS 1 x UMS
Ligand T5S 1 x T5S

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P43212
Unit cell:
a: 43.078Å b: 43.078Å c: 23.814Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.175 0.2
Expression system: Not provided

Quick links

Citations

1 review citation

Membrane linked RNA glycosylation as new trend to envision epi-transcriptome epoch.
Tyagi et al. (2022)
6 other articles

2 mentions without citation

Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.
Sheng et al. (2012)
1 more