› 1yls

X-ray diffraction
3Å resolution

Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene

Released:
DOI: 10.2210/pdb1yls/pdb
PDB entry 1yls coloured by chain, front view.
PDB entry 1yls coloured by chain, side view.
PDB entry 1yls coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.
Serganov A, Keiper S, Malinina L, Tereshko V, Skripkin E, Höbartner C, Polonskaia A, Phan AT, Wombacher R, Micura R, Dauter Z, Jäschke A, Patel DJ
Nat Struct Mol Biol 12 218-24 (2005)
PMID: 15723077

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-196265 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
RNA Diels-Alder ribozyme Chains: A, C
Molecule details ›
Chains: A, C
Length: 11 nucleotides
Theoretical weight: 3.65 KDa
Source organism: Synthetic construct
Expression system: Not provided
RNA Diels-Alder ribozyme Chains: B, D
Molecule details ›
Chains: B, D
Length: 38 nucleotides
Theoretical weight: 12.59 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DAI 2 x DAI
Ligand MG 13 x MG
2 modified residues:
Ligand UMS 6 x UMS
Ligand CSL 6 x CSL

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 77.873Å b: 43.269Å c: 79.928Å
α: 90° β: 106.19° γ: 90°
R-values:
R R work R free
0.21 0.209 0.234
Expression system: Not provided

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Citations

38 review citations

Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.
Patel et al. (2007)
37 more

7 mentions without citation

Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.
Serganov et al. (2005)
6 more