Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb1vsp1w.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
Source: Resolution 3.83 ANGSTROMS.
Position (728, 756), (733, 750)
Primary structure ('_': anchors) _UGAA_-_GGAGG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-exo, 2: C2'-exo, 5: C2'-exo, 9: C2'-exo, 11: C4'-exo, 12: C3'-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 2 ↑
2 3 9 &larr
3 4 5 ↑
4 4 10 →
5 5 6 ↑
6 7 8 ↑
7 8 9 ↑
8 10 11 ↑
9 11 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 11 Watson-Crick/Watson-Crick cis
3 3 10 O2'/Bifurcated trans
4 4 8 Watson-Crick/O2' ?
5 4 9 O2'/Bifurcated trans
6 5 8 O2'/Bifurcated trans
7 6 7 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters