› 3gs5

X-ray diffraction
2.75Å resolution

An all-RNA hairpin ribozyme A38N1dA variant with a product mimic substrate strand

Released:
DOI: 10.2210/pdb3gs5/pdb
PDB entry 3gs5 coloured by chain, front view.
PDB entry 3gs5 coloured by chain, side view.
PDB entry 3gs5 coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Identification of an imino group indispensable for cleavage by a small ribozyme.
Spitale RC, Volpini R, Heller MG, Krucinska J, Cristalli G, Wedekind JE
J Am Chem Soc 131 6093-5 (2009)
PMID: 19354216

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-196679 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
RNA (25-MER) Chain: A
Molecule details ›
Chain: A
Length: 25 nucleotides
Theoretical weight: 8.07 KDa
Source organism: Synthetic construct
Expression system: Not provided
RNA (36-MER) Chain: C
Molecule details ›
Chain: C
Length: 36 nucleotides
Theoretical weight: 11.57 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand S9L 1 x S9L
Ligand NCO 2 x NCO
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH2R
Spacegroup: P6122
Unit cell:
a: 93.83Å b: 93.83Å c: 132.09Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.218 0.218 0.243
Expression system: Not provided

Quick links

Citations

4 review citations

The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.
Šponer et al. (2012)
3 more