Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'7-9-Internal Loop pdb1m5p1B.n27-54
Source: [PDB-id:chain] 1m5p:B (&rarr PDB)
Source: Information TRANSITION STATE STABILIZATION BY A CATALYTIC RNA
Source: Compound RNA HAIRPIN RIBOZYME
Source: Resolution 2.60 ANGSTROMS.
Position (19, 64), (27, 54)
Primary structure ('_': anchors) _AGAAACA_-_GUAUAUUAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		11: C3'-exo, 12: C2'-endo, 13: C3'-exo, 14: C3'-exo, 16: C4'-exo, 17: C3'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		13: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 16 &larr
4 4 5 ↑
5 4 18 →
6 5 6 ↑
7 6 7 ↑
8 7 8 ↑
9 8 9 ↑
10 10 11 ↑
11 13 15 ↑
12 15 16 ↑
13 18 19 ↑
14 19 20 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 20 Watson-Crick/Watson-Crick cis
2 2 19 Watson-Crick/Watson-Crick cis
3 3 18 Bifurcated/O2' trans
4 4 16 Watson-Crick/Hoogsteen trans
5 5 15 Watson-Crick/Hoogsteen trans
6 5 17 Watson-Crick/Watson-Crick cis y
7 6 13 Hoogsteen/Watson-Crick trans y
8 8 11 Watson-Crick/Watson-Crick cis
9 9 10 Watson-Crick/Watson-Crick cis
10 16 17 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters