Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb2e5l1A.n398-428
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
Source: Resolution 3.30 ANGSTROMS.
Position (401, 425), (408, 419)
Primary structure ('_': anchors) _GAAGAA_-_GUAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 4: O4'-endo, 10: C4'-exo, 11: O4'-endo, 12: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 5 ↑
3 3 11 →
4 6 7 ↑
5 7 8 ↑
6 9 10 &larr
7 10 12 →
8 12 13 ↑
9 13 14 ↑
10 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 2 13 O2'/Watson-Crick ?
3 2 14 Bifurcated/O2' trans y
4 3 5 O2'/Sugar ?
5 3 12 Hoogsteen/Watson-Crick trans
6 5 10 O2'/Bifurcated trans
7 6 10 Bifurcated/O2' ?
8 7 10 Hoogsteen/Hoogsteen trans y
9 8 9 Watson-Crick/Watson-Crick cis y
10 11 13 Hoogsteen/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters