Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb1ykvFD.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
FLIPPED INTERNAL
Source: Resolution 3.30 ANGSTROMS.
Position (11, 35), (17, 28)
Primary structure ('_': anchors) _AAUACU_-_UGCCA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 4: O4'-endo, 9: C2'-exo, 13: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 4 ↑
2 5 6 ↑
3 5 13 &larr
4 6 7 ↑
5 7 8 ↑
6 9 10 ↑
7 10 11 ↑
8 13 14 ↑
9 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 2 Bifurcated/O2' ?
2 1 15 Watson-Crick/Watson-Crick cis
3 2 4 O2'/Sugar ?
4 4 13 O2'/Bifurcated ?
5 4 14 Hoogsteen/Watson-Crick trans y
6 5 12 Bifurcated/Hoogsteen trans
7 5 13 Watson-Crick/O2' ?
8 6 13 Bifurcated/O2' ?
9 7 10 Watson-Crick/Watson-Crick cis y
10 8 9 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters