Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'19-Hairpin pdb1vsp1w.e178-198
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 (178, 198)
Primary structure ('_': anchors) _GAACUGAAACAUCUCAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 6: C2'-exo, 8: C2'-exo, 9: C4'-exo, 12: C3'-exo, 14: C2'-exo, 15: C4'-exo, 17: C4'-exo, 18: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		9: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 18 &larr
3 3 4 ↑
4 3 20 →
5 4 5 ↑
6 5 6 ↑
7 7 8 ↑
8 10 11 ↑
9 13 14 ↑
10 15 16 ↑
11 16 17 &larr
12 17 19 →
13 19 20 ↑
14 20 21 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 21 Watson-Crick/Watson-Crick cis
2 2 18 O2'/Bifurcated ?
3 2 20 Bifurcated/O2' ?
4 3 18 Bifurcated/O2' ?
5 6 15 Watson-Crick/Watson-Crick cis y
6 7 14 Watson-Crick/Watson-Crick cis
7 8 11 O2'/Hoogsteen ?
8 11 12 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters