Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'7-7-Internal Loop pdb1d6kFB.n13-26
Source: [PDB-id:chain] 1d6k:B (&rarr PDB)
Source: Information NMR SOLUTION STRUCTURE OF THE 5S RRNA E-LOOP/L25 COMPLEX
Source: Compound 5S RRNA E-LOOP (5SE)
FLIPPED INTERNAL
Source: Resolution NOT APPLICABLE.
Position (5, 34), (13, 26)
Primary structure ('_': anchors) _GAGAGUA_-_GAUGGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		7: C1'-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 2 16 →
4 3 4 ↑
5 4 5 ↑
6 5 6 ↑
7 6 7 ↑
8 7 11 →
9 10 11 ↑
10 11 12 ↑
11 12 13 ↑
12 13 14 ↑
13 14 15 ↑
14 15 16 ↑
15 17 18 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 18 Watson-Crick/Watson-Crick cis
2 2 17 Bifurcated/O2' trans
3 3 16 Watson-Crick/Hoogsteen trans
4 3 17 O2'/Watson-Crick ?
5 4 15 Watson-Crick/Hoogsteen trans y
6 6 13 Bifurcated/Watson-Crick trans
7 7 12 Hoogsteen/Watson-Crick trans
8 8 11 O2'/Bifurcated trans
9 9 10 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters