Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-4-Internal Loop pdb2e5lFA.n239-269
Source: [PDB-id:chain] 2e5l:A (&rarr PDB)
Source: Information A SNAPSHOT OF THE 30S RIBOSOMAL SUBUNIT CAPTURING MRNA VIA THE SHINE- DALGARNO INTERACTION
Source: Compound 16S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.30 ANGSTROMS.
Position (234, 276), (239, 269)
Primary structure ('_': anchors) _GACGAC_-_AUCA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 5: O4'-endo, 10: O4'-endo, 12: O4'-endo, 13: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 1 11 →
3 2 3 ↑
4 3 10 →
5 6 10 ↑
6 7 9 →
7 10 13 ↑
8 11 13 ↓
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 2 3 Bifurcated/O2' ?
3 2 11 Watson-Crick/Watson-Crick cis y
4 3 9 Watson-Crick/O2' trans y
5 3 13 Hoogsteen/Watson-Crick trans y
6 4 10 Sugar/Hoogsteen trans
7 4 13 O2'/Bifurcated ?
8 7 10 O2'/Watson-Crick trans y
9 8 9 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters