Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb1fqz1A.n9-20
Source: [PDB-id:chain] 1fqz:A (&rarr PDB)
Source: Information NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE
Source: Compound HEPATITIS C VIRUS IRES DOMAIN IIID
Source: Resolution NOT APPLICABLE.
Position (3, 25), (9, 20)
Primary structure ('_': anchors) _GAGUA_-_GAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 4: C2'-endo, 10: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		4: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 &larr
3 3 5 →
4 4 9 &larr
5 5 6 ↑
6 6 7 ↑
7 6 10 →
8 8 9 ↑
9 10 11 ↑
10 11 12 ↑
11 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 12 Bifurcated/O2' trans
3 3 11 O2'/Bifurcated trans
4 4 5 Hoogsteen/Sugar cis y
5 4 10 O2'/Bifurcated ?
6 5 9 Watson-Crick/O2' ?
7 5 10 Hoogsteen/Watson-Crick trans
8 6 9 O2'/Bifurcated trans
9 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters