Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'2-3-Internal Loop pdb1ebr1A.n1-30
Source: [PDB-id:chain] 1ebr:A (&rarr PDB)
Source: Information STRUCTURE OF RNA (5'-GGUGGGCGCAGCUUCGGCUGCGGUACCAC-3'), NMR, 5 STRUCTURES
Source: Compound HIV-1 REV RESPONSIVE ELEMENT RNA
Source: Resolution NOT APPLICABLE.
Position (4, 27), (7, 23)
Primary structure ('_': anchors) _GG_-_GUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C3'-exo, 3: O4'-endo, 6: C3'-exo, 7: C2'-endo, 8: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		6: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 6 8 →
3 8 9 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 9 Watson-Crick/Watson-Crick cis
2 2 3 Hoogsteen/O2' ?
3 2 8 Watson-Crick/Watson-Crick cis
4 3 4 Bifurcated/O2' ?
5 3 6 Watson-Crick/Watson-Crick trans
6 4 5 Watson-Crick/Watson-Crick cis
7 5 6 Bifurcated/O2' ?
8 6 8 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters