Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-5-Internal Loop pdb1yl3FA.n2616-2751
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 (2610, 2761), (2616, 2751)
Primary structure ('_': anchors) _AAGAUGAGG_-_CUUGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 3: C2'-exo, 4: C4'-exo, 6: C2'-exo, 8: C1'-endo, 14: C4'-exo, 15: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		8: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 7 13 →
4 10 11 ↑
5 10 12 →
6 10 14 &larr
7 12 13 ↑
8 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 18 Watson-Crick/Watson-Crick cis
2 3 16 Watson-Crick/Watson-Crick cis
3 4 6 Bifurcated/O2' ?
4 9 14 O2'/Watson-Crick ?
5 10 13 Sugar/Hoogsteen trans
6 11 12 Watson-Crick/Watson-Crick cis
7 12 13 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters