Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'17-Hairpin pdb1c041F.e6-24
Source: [PDB-id:chain] 1c04:F (&rarr PDB)
Source: Information IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI
Source: Compound 23S RRNA FRAGMENT
Source: Resolution 5.00 ANGSTROMS.
Position (6, 24)
Primary structure ('_': anchors) _UCAGUACGAGAGGAACC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C4'-exo, 4: C2'-endo, 5: C2'-endo, 6: C2'-exo, 12: 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 4 &larr
3 4 6 →
4 5 14 &larr
5 6 7 ↑
6 7 8 ↑
7 7 15 →
8 8 9 ↑
9 9 13 →
10 10 11 ↑
11 11 12 ↑
12 13 14 ↑
13 15 16 ↑
14 16 17 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 19 Watson-Crick/Watson-Crick cis
2 2 18 Hoogsteen/Watson-Crick trans y
3 4 16 O2'/Bifurcated ?
4 5 6 Hoogsteen/Sugar cis y
5 5 14 Watson-Crick/O2' ?
6 5 15 O2'/Bifurcated ?
7 6 14 Bifurcated/O2' ?
8 6 15 Hoogsteen/Watson-Crick trans
9 7 14 Sugar/Hoogsteen trans
10 8 13 Watson-Crick/Watson-Crick cis
11 9 11 Hoogsteen/O2' ?
12 9 12 O2'/Bifurcated trans
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters