Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-6-Internal Loop pdb1j5e1A.n231-277
Source: [PDB-id:chain] 1j5e:A (&rarr PDB)
Source: Information STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT
Source: Compound 16S RIBOSOMAL RNA
Source: Resolution 3.05 ANGSTROMS.
Position (233, 275), (238, 268)
Primary structure ('_': anchors) _AUCA_-_GACGAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C1'-exo, 3: C2'-endo, 5: C2'-endo, 10: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 4 ↓
2 2 5 ↑
3 4 14 →
4 5 9 ↑
5 5 12 →
6 6 8 →
7 7 8 ↑
8 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 2 11 O2'/Bifurcated ?
3 2 12 Hoogsteen/Watson-Crick trans
4 4 13 Watson-Crick/Watson-Crick cis y
5 5 8 O2'/Watson-Crick ?
6 5 11 Sugar/Hoogsteen trans
7 6 7 Watson-Crick/Watson-Crick cis
8 6 12 Watson-Crick/O2' trans y
9 11 12 Hoogsteen/O2' ?
10 12 13 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters