› 4u6m

X-ray diffraction
1.9Å resolution

Crystal structure of DNA/RNA duplex obtained in the presence of Spermine

Released:
DOI: 10.2210/pdb4u6m/pdb
PDB entry 4u6m coloured by chain, front view.
PDB entry 4u6m coloured by chain, side view.
PDB entry 4u6m coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
The crystal structure of a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer in complex with the target RNA.
Kondo J, Nomura Y, Kitahara Y, Obika S, Torigoe H
Chem Commun (Camb) 52 2354-7 (2016)
PMID: 26731288

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-118179 (preferred)
Entry contents:
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3') Chain: B
Molecule details ›
Chain: B
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: A
Molecule details ›
Chain: A
Length: 9 nucleotides
Theoretical weight: 2.98 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P61
Unit cell:
a: 49.09Å b: 49.09Å c: 45.99Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.206 0.233
Expression system: Not provided

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