Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'15-Hairpin pdb1vq510.e1735-1751
Source: [PDB-id:chain] 1vq5:0 (&rarr PDB)
Source: Information THE STRUCTURE OF THE TRANSITION STATE ANALOGUE "RAA" BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.60 ANGSTROMS.
Position (1735, 1751)
Primary structure ('_': anchors) _GUACCUUCGGAAGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		8: C2'-endo, 9: C2'-endo, 13: C2'-endo, 14: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		10: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 4 5 ↑
4 4 15 →
5 5 6 ↑
6 6 7 ↑
7 10 11 →
8 11 12 ↑
9 12 13 &larr
10 15 16 ↑
11 16 17 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 17 Watson-Crick/Watson-Crick cis
2 2 15 O2'/Watson-Crick ?
3 2 16 Bifurcated/O2' trans
4 3 15 Hoogsteen/O2' ?
5 4 13 O2'/Bifurcated trans
6 5 12 Sugar/Hoogsteen trans y
7 6 11 Watson-Crick/Watson-Crick cis
8 7 10 Watson-Crick/Watson-Crick trans y
9 8 9 Bifurcated/O2' ?
10 8 10 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters