Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb1p5n1A.n9-25
Source: [PDB-id:chain] 1p5n:A (&rarr PDB)
Source: Information SOLUTION STRUCTURE OF HCV IRES DOMAIN IIB
Source: Compound 34-MER
Source: Resolution NOT APPLICABLE.
Position (4, 31), (9, 25)
Primary structure ('_': anchors) _GAAA_-_UAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		9: C2'-endo, 10: 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 3 4 ↑
3 3 12 →
4 4 5 ↑
5 5 6 ↑
6 7 8 ↑
7 8 9 &larr
8 9 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 11 O2'/Watson-Crick ?
3 2 12 Hoogsteen/Sugar trans
4 3 11 Watson-Crick/Hoogsteen trans
5 4 9 Hoogsteen/Hoogsteen trans
6 5 8 O2'/Bifurcated trans y
7 6 7 Watson-Crick/Watson-Crick cis
8 6 8 O2'/Bifurcated ?
9 10 11 Hoogsteen/Sugar cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters