Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-7-Internal Loop pdb1ibm1A.n667-678
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 (662, 686), (667, 678)
Primary structure ('_': anchors) _AGUA_-_GCAGAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C1'-exo, 5: O4'-endo, 6: C2'-exo, 9: C2'-endo, 10: C2'-endo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 5 9 ↑
5 5 12 →
6 6 8 →
7 7 8 ↑
8 9 11 →
9 12 13 ↑
10 13 14 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 2 14 Watson-Crick/Watson-Crick cis y
3 3 12 O2'/Bifurcated ?
4 3 13 Hoogsteen/Sugar trans y
5 4 12 Hoogsteen/Watson-Crick trans
6 5 8 O2'/Watson-Crick trans y
7 5 11 Sugar/Hoogsteen trans y
8 6 7 Watson-Crick/Watson-Crick cis
9 6 12 Watson-Crick/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters