Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb1ykv1D.n17-28
Source: [PDB-id:chain] 1ykv:D (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE DIELS-ALDER RIBOZYME COMPLEXED WITH THE PRODUCT OF THE REACTION BETWEEN N-PENTYLMALEIMIDE AND COVALENTLY ATTACHED 9-HYDROXYMETHYLANTHRACENE
Source: Compound DIELS-ALDER RIBOZYME
Source: Resolution 3.30 ANGSTROMS.
Position (11, 35), (17, 28)
Primary structure ('_': anchors) _UGCCA_-_AAUACU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 7: C2'-exo, 12: O4'-endo, 14: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 11 &larr
4 5 6 ↑
5 6 7 ↑
6 8 9 ↑
7 9 10 ↑
8 10 11 ↑
9 12 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 2 12 Hoogsteen/Watson-Crick trans y
3 3 10 Bifurcated/O2' ?
4 3 11 Watson-Crick/O2' ?
5 3 12 O2'/Bifurcated ?
6 4 11 Bifurcated/Hoogsteen trans
7 6 9 Watson-Crick/Watson-Crick cis y
8 7 8 Watson-Crick/Watson-Crick cis
9 12 14 O2'/Sugar ?
10 14 15 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters