Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-7-Internal Loop pdb1m5kFE.n27-54
Source: [PDB-id:chain] 1m5k:E (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF A HAIRPIN RIBOZYME IN THE CATALYTICALLY-ACTIVE CONFORMATION
Source: Compound RNA HAIRPIN RIBOZYME
FLIPPED INTERNAL
Source: Resolution 2.40 ANGSTROMS.
Position (19, 64), (27, 54)
Primary structure ('_': anchors) _GUAUAUUAC_-_AGAAACA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C3'-exo, 5: C4'-exo, 7: C2'-endo, 8: C3'-exo, 9: C3'-exo, 10: C3'-exo, 13: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		8: syn, 10: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 17 →
4 5 6 ↑
5 5 18 &larr
6 6 8 ↑
7 10 11 ↑
8 12 13 ↑
9 13 14 ↑
10 14 15 ↑
11 15 16 ↑
12 16 17 ↑
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 y
3 3 18 Bifurcated/O2' trans y
4 4 5 Hoogsteen/O2' ?
5 4 16 Watson-Crick/Watson-Crick cis
6 4 17 Watson-Crick/Watson-Crick trans y
7 5 17 Watson-Crick/Hoogsteen trans
8 6 16 Watson-Crick/Hoogsteen trans
9 8 15 Hoogsteen/Watson-Crick trans y
10 10 13 Watson-Crick/Watson-Crick cis
11 11 12 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters