› 2dpb

X-ray diffraction
1.5Å resolution

Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine

Released:
DOI: 10.2210/pdb2dpb/pdb
PDB entry 2dpb coloured by chain, front view.
PDB entry 2dpb coloured by chain, side view.
PDB entry 2dpb coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules.
Juan EC, Kondo J, Kurihara T, Ito T, Ueno Y, Matsuda A, Takénaka A
Nucleic Acids Res 35 1969-77 (2007)
PMID: 17341465

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-115177 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DUP*DCP*DGP*DCP*DG)-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 12 nucleotides
Theoretical weight: 3.65 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CMY 2 x CMY
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-18B
Spacegroup: P212121
Unit cell:
a: 25.539Å b: 40.833Å c: 64.456Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.193 0.245
Expression system: Not provided

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Citations

4 review citations

Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.
Egli et al. (2007)
3 more

1 mention without citation

Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules.
Juan et al. (2007)