Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-9-Internal Loop pdb1yl3FA.n1858-1893
Source: [PDB-id:chain] 1yl3:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF 70S RIBOSOME WITH THRS OPERATOR AND TRNAS. LARGE SUBUNIT. THE COORDINATES FOR THE SMALL SUBUNIT ARE IN THE PDB ENTRY 1YL4.
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 5.50 ANGSTROMS.
Position (1860, 1891), (1870, 1881)
Primary structure ('_': anchors) _CGAACCGAA_-_CAAGGGGAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 8: C2'-exo, 9: C4'-exo, 11: C2'-exo, 18: C2'-exo, 21: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		4: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 4 5 &larr
4 5 17 →
5 6 7 ↑
6 7 15 →
7 12 13 ↑
8 17 18 ↑
9 18 19 ↑
10 19 20 ↑
11 21 22 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 22 Watson-Crick/Watson-Crick cis
2 3 21 Hoogsteen/Watson-Crick trans y
3 6 17 Watson-Crick/Watson-Crick cis
4 7 16 Bifurcated/O2' ?
5 8 14 O2'/Watson-Crick ?
6 8 15 O2'/Bifurcated ?
7 8 16 Watson-Crick/Watson-Crick cis y
8 9 14 O2'/Bifurcated trans
9 11 12 Watson-Crick/Watson-Crick cis
10 16 17 Sugar/Hoogsteen trans y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters