Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-1-Internal Loop pdb1f1tFA.n10-23
Source: [PDB-id:chain] 1f1t:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE
Source: Compound MALACHITE GREEN APTAMER RNA
FLIPPED INTERNAL
Source: Resolution 2.80 ANGSTROMS.
Position (8, 28), (10, 23)
Primary structure ('_': anchors) _GUAA_-_A_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-exo, 5: C1'-exo, 9: C1'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 7 9 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 4 O2'/Watson-Crick ?
2 1 6 Bifurcated/O2' ?
3 1 9 Watson-Crick/Watson-Crick cis
4 2 4 O2'/Watson-Crick ?
5 2 6 Watson-Crick/Sugar trans
6 6 7 Watson-Crick/Watson-Crick cis
7 7 9 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters