› 2dqq

X-ray diffraction
2Å resolution

Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine

Released:
DOI: 10.2210/pdb2dqq/pdb
PDB entry 2dqq coloured by chain, front view.
PDB entry 2dqq coloured by chain, side view.
PDB entry 2dqq 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:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-115185 (preferred)
Entry contents:
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
DNA (5'-D(*DCP*(OMU)P*DCP*DTP*(OMU)P*DCP*DTP*DTP*DC)-3') Chain: A
Molecule details ›
Chain: A
Length: 9 nucleotides
Theoretical weight: 2.66 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.98 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CMY 2 x CMY
1 modified residue:
Ligand OMU 2 x OMU

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-18B
Spacegroup: P61
Unit cell:
a: 52.471Å b: 52.471Å c: 42.488Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.246 0.246 0.284
Expression system: Not provided

Quick links

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)