Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb1ibl1A.n397-427
Source: [PDB-id:chain] 1ibl:A (&rarr PDB)
Source: Information STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE AND WITH THE ANTIBIOTIC PAROMOMYCIN
Source: Compound 16S RIBOSOMAL RNA
Source: Resolution 3.11 ANGSTROMS.
Position (400, 424), (407, 418)
Primary structure ('_': anchors) _GAAGAA_-_GUAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C4'-exo, 5: C4'-exo, 10: C4'-exo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 11 &larr
3 3 5 ↑
4 6 7 ↑
5 6 13 →
6 7 8 ↑
7 9 10 &larr
8 10 12 →
9 12 13 ↑
10 13 14 ↑
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 11 O2'/Hoogsteen ?
3 2 13 O2'/Watson-Crick ?
4 2 14 Bifurcated/O2' trans
5 3 5 O2'/Sugar ?
6 3 12 Hoogsteen/Watson-Crick trans y
7 5 10 O2'/Bifurcated ?
8 5 11 O2'/Watson-Crick ?
9 6 10 Bifurcated/O2' ?
10 7 10 Hoogsteen/Hoogsteen trans y
11 8 9 Watson-Crick/Watson-Crick cis
12 11 13 Hoogsteen/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters