Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb1ysh1F.n17-27
Source: [PDB-id:chain] 1ysh:F (&rarr PDB)
Source: Information LOCALIZATION AND DYNAMIC BEHAVIOR OF RIBOSOMAL PROTEIN L30E
Source: Compound RNA (34-MER)
Source: Resolution 9.50 ANGSTROMS.
Position (12, 33), (17, 27)
Primary structure ('_': anchors) _GGAA_-_AGGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 5: C4'-exo, 6: C2'-endo, 9: C2'-endo, 10: O4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn, 5: syn, 6: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 10 &larr
3 4 8 ↑
4 4 11 →
5 5 8 ↓
6 11 12 ↑
7 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 11 O2'/Bifurcated ?
3 2 12 Bifurcated/O2' trans
4 3 10 O2'/Bifurcated ?
5 3 11 O2'/Bifurcated trans y
6 4 7 O2'/Watson-Crick trans y
7 4 10 O2'/Bifurcated trans
8 6 7 Watson-Crick/Watson-Crick cis
9 10 11 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters