Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'19-Hairpin pdb1kqs10.e150-170
Source: [PDB-id:chain] 1kqs:0 (&rarr PDB)
Source: Information THE HALOARCULA MARISMORTUI 50S COMPLEXED WITH A PRETRANSLOCATIONAL INTERMEDIATE IN PROTEIN SYNTHESIS
Source: Compound 23S RRNA
Source: Resolution 3.10 ANGSTROMS.
Position (150, 170)
Primary structure ('_': anchors) _GAACUGAAACAUCUCAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		9: C1'-exo, 12: C3'-exo, 17: C2'-endo, 18: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		9: syn, 12: 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 6 7 ↑
7 7 8 ↑
8 8 11 &larr
9 10 11 ↑
10 13 14 ↑
11 14 15 ↑
12 15 16 ↑
13 16 17 &larr
14 17 19 →
15 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'/Watson-Crick ?
3 2 19 O2'/Watson-Crick ?
4 2 20 Bifurcated/O2' trans
5 3 18 Bifurcated/O2' ?
6 3 19 Watson-Crick/Hoogsteen trans
7 4 17 Bifurcated/O2' trans
8 5 16 O2'/Bifurcated trans
9 6 15 Watson-Crick/Watson-Crick cis
10 7 14 Watson-Crick/Watson-Crick cis
11 8 10 O2'/Hoogsteen ?
12 8 11 O2'/Bifurcated ?
13 8 12 O2'/Bifurcated ?
14 8 13 Hoogsteen/Bifurcated trans y
15 10 11 Bifurcated/O2' ?
16 18 19 Hoogsteen/Sugar cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters