Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-7-Internal Loop pdb1y69F0.n1717-1753
Source: [PDB-id:chain] 1y69:0 (&rarr PDB)
Source: Information RRF DOMAIN I IN COMPLEX WITH THE 50S RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.33 ANGSTROMS.
Position (1721, 1749), (1729, 1739)
Primary structure ('_': anchors) _GACGUAUAG_-_CUGCCAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C4'-exo, 7: C2'-exo, 9: C4'-exo, 10: C2'-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 6 7 ↑
4 7 9 →
5 10 11 ↑
6 12 13 ↑
7 13 14 ↑
8 18 19 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 20 Watson-Crick/Watson-Crick cis
2 2 13 O2'/Watson-Crick trans
3 3 5 Hoogsteen/O2' ?
4 3 18 Watson-Crick/Watson-Crick cis
5 5 17 O2'/Bifurcated ?
6 9 14 Bifurcated/O2' ?
7 10 13 O2'/Bifurcated trans
8 11 12 Watson-Crick/Watson-Crick cis
9 14 18 Sugar/O2' cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters