Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'13-Hairpin pdb1vq919.e33-47
Source: [PDB-id:chain] 1vq9:9 (&rarr PDB)
Source: Information THE STRUCTURE OF CCA-PHE-CAP-BIO AND THE ANTIBIOTIC SPARSOMYCIN BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 5S RIBOSOMAL RNA
Source: Resolution 2.40 ANGSTROMS.
Position (33, 47)
Primary structure ('_': anchors) _ACCCAUCCCGAAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-endo, 7: C4'-exo, 8: C4'-exo, 9: C4'-exo, 11: C3'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 11 &larr
2 2 3 ↑
3 4 5 ↑
4 6 11 →
5 9 10 ↑
6 10 12 ↑
7 11 15 ↑
8 12 13 ↑
9 13 14 ↑
10 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 11 Hoogsteen/O2' ?
2 1 15 Watson-Crick/Watson-Crick cis
3 4 15 O2'/Watson-Crick cis y
4 5 11 Watson-Crick/Watson-Crick cis
5 6 13 Watson-Crick/O2' cis y
6 7 10 Bifurcated/O2' ?
7 7 12 Bifurcated/O2' ?
8 8 10 Bifurcated/O2' ?
9 11 14 Watson-Crick/Sugar trans
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters