Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb1pnxFA.n411-422
Source: [PDB-id:chain] 1pnx:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE WILD TYPE RIBOSOME FROM E. COLI, 30S SUBUNIT OF 70S RIBOSOME. THIS FILE, 1PNX, CONTAINS ONLY MOLECULES OF THE 30S RIBOSOMAL SUBUNIT. THE 50S SUBUNIT IS IN THE PDB FILE 1PNY.
Source: Compound 16S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 9.50 ANGSTROMS.
Position (404, 428), (411, 422)
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 4 6 →
5 5 14 &larr
6 6 7 &larr
7 8 9 ↑
8 9 10 ↑
9 11 13 ↑
10 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 Bifurcated/O2' trans
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
7 5 11 O2'/Bifurcated ?
8 5 14 O2'/Hoogsteen ?
9 6 9 Hoogsteen/Hoogsteen trans y
10 6 10 Bifurcated/O2' ?
11 6 11 Bifurcated/O2' 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