Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-8-Internal Loop pdb1ibm1A.n1230-1261
Source: [PDB-id:chain] 1ibm: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
Source: Compound 16S RIBOSOMAL RNA
Source: Resolution 3.31 ANGSTROMS.
Position (1232, 1259), (1239, 1250)
Primary structure ('_': anchors) _AUGCCA_-_GAGCUAAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C4'-exo, 15: C4'-exo, 16: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		2: syn, 15: syn, 17: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 15 ↑
2 4 5 ↑
3 5 6 ↑
4 7 8 ↑
5 7 11 →
6 9 10 ↑
7 11 12 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 4 Sugar/O2' ?
2 1 18 Watson-Crick/Watson-Crick cis
3 2 15 Bifurcated/O2' ?
4 3 4 Hoogsteen/O2' ?
5 5 12 Watson-Crick/Watson-Crick cis y
6 6 11 Bifurcated/Bifurcated trans y
7 7 10 Sugar/Hoogsteen trans
8 8 9 Watson-Crick/Watson-Crick cis
9 12 18 O2'/Sugar ?
10 15 18 Bifurcated/O2' ?
11 17 18 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters