Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb1p5nFA.n9-25
Source: [PDB-id:chain] 1p5n:A (&rarr PDB)
Source: Information SOLUTION STRUCTURE OF HCV IRES DOMAIN IIB
Source: Compound 34-MER
FLIPPED INTERNAL
Source: Resolution NOT APPLICABLE.
Position (4, 31), (9, 25)
Primary structure ('_': anchors) _UAGUA_-_GAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-endo, 5: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 11 →
3 3 5 →
4 5 6 &larr
5 6 7 ↑
6 8 9 ↑
7 9 10 ↑
8 10 11 ↑
9 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis y
2 2 12 Hoogsteen/Sugar trans
3 3 4 Hoogsteen/Sugar cis y
4 3 11 Watson-Crick/Hoogsteen trans
5 3 12 O2'/Watson-Crick ?
6 5 10 Hoogsteen/Hoogsteen trans
7 6 8 O2'/Bifurcated ?
8 6 9 O2'/Bifurcated trans y
9 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters