Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb1ykv1B.n17-28
Source: [PDB-id:chain] 1ykv:B (&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, 12: C4'-exo, 13: C1'-endo, 14: C1'-exo
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
3 3 11 Watson-Crick/O2' ?
4 3 12 O2'/Watson-Crick ?
5 4 11 Sugar/Hoogsteen trans y
6 7 8 Watson-Crick/Watson-Crick cis
7 14 15 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters