Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb1vspFw.n726-758
Source: [PDB-id:chain] 1vsp:w (&rarr PDB)
Source: Information INTERACTIONS AND DYNAMICS OF THE SHINE-DALGARNO HELIX IN THE 70S RIBOSOME. THIS FILE, 1VSP, CONTAINS THE 50S RIBOSOME SUBUNIT. 30S RIBOSOME SUBUNIT IS IN THE FILE 2QNH
Source: Compound 23S LARGE SUBUNIT RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.83 ANGSTROMS.
Position (728, 756), (733, 750)
Primary structure ('_': anchors) _GGAGG_-_UGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-exo, 2: C3'-exo, 3: C4'-exo, 5: C2'-exo, 9: C2'-exo, 12: C2'-exo, 13: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 3 ↑
2 3 4 ↑
3 4 10 →
4 5 6 ↑
5 5 11 &larr
6 6 7 ↑
7 8 9 ↑
8 9 10 ↑
9 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 3 12 Watson-Crick/Watson-Crick cis
3 4 11 O2'/Bifurcated trans
4 5 10 O2'/Bifurcated trans
5 6 9 O2'/Bifurcated trans
6 6 10 Watson-Crick/O2' ?
7 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters