› 1i7j

X-ray diffraction
1.19Å resolution

CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.19 A RESOLUTION. 2-METHYL-2,4-PENTANEDIOL AND MAGNESIUM BINDING.

Released:
DOI: 10.2210/pdb1i7j/pdb
PDB entry 1i7j coloured by chain, front view.
PDB entry 1i7j coloured by chain, side view.
PDB entry 1i7j coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove.
Adamiak DA, Rypniewski WR, Milecki J, Adamiak RW
Nucleic Acids Res 29 4144-53 (2001)
PMID: 11600703

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-196051 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 6 nucleotides
Theoretical weight: 1.99 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 5 x MG
Ligand MPD 2 x MPD
2 modified residues:
Ligand OMC 6 x OMC
Ligand OMG 6 x OMG

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7A
Spacegroup: P3212
Unit cell:
a: 24.805Å b: 24.805Å c: 77.372Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.155 0.155 not available
Expression system: Not provided

Quick links

Citations

1 review citation

RNA Structural Differentiation: Opportunities with Pattern Recognition.
Eubanks et al. (2019)
16 other articles

1 mention without citation

RLDOCK method for predicting RNA-small molecule binding modes.
Jiang et al. (2022)