Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'2-6-Internal Loop pdb2vpl1D.n12-33
Source: [PDB-id:chain] 2vpl:D (&rarr PDB)
Source: Information THE STRUCTURE OF THE COMPLEX BETWEEN THE FIRST DOMAIN OF L1 PROTEIN FROM THERMUS THERMOPHILUS AND MRNA FROM METHANOCOCCUS JANNASCHII
Source: Compound FRAGMENT OF MRNA FOR L1-OPERON CONTAINING
Source: Resolution 2.30 ANGSTROMS.
Position (9, 40), (12, 33)
Primary structure ('_': anchors) _GA_-_GAGAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 7: C2'-exo, 8: O4'-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 11 →
3 4 6 →
4 5 6 ↑
5 6 7 ↑
6 9 10 ↑
7 11 12 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 12 Watson-Crick/Watson-Crick cis
2 2 10 O2'/Watson-Crick ?
3 2 11 Bifurcated/O2' trans
4 3 6 O2'/Watson-Crick ?
5 4 5 Watson-Crick/Watson-Crick cis
6 4 11 Watson-Crick/O2' trans y
7 8 10 Hoogsteen/O2' ?
8 11 12 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters