Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb1ibkFA.n407-418
Source: [PDB-id:chain] 1ibk:A (&rarr PDB)
Source: Information STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH THE ANTIBIOTIC PAROMOMYCIN
Source: Compound 16S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.31 ANGSTROMS.
Position (400, 424), (407, 418)
Primary structure ('_': anchors) _GUAAA_-_GAAGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-endo, 6: C2'-endo, 11: C4'-exo, 12: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 13: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 3 10 →
5 4 6 →
6 5 14 &larr
7 6 7 &larr
8 8 9 ↑
9 9 10 ↑
10 11 13 ↑
11 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 14 Hoogsteen/Sugar trans y
3 3 5 Hoogsteen/Watson-Crick cis
4 3 14 O2'/Watson-Crick ?
5 4 10 Watson-Crick/Hoogsteen trans y
6 4 13 Hoogsteen/Watson-Crick trans y
7 5 11 O2'/Bifurcated ?
8 5 14 O2'/Hoogsteen ?
9 6 9 Bifurcated/Hoogsteen trans y
10 6 10 Bifurcated/O2' ?
11 6 11 Sugar/Sugar trans
12 7 8 Watson-Crick/Watson-Crick cis
13 11 13 O2'/Sugar ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters