Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'2-9-Internal Loop pdb2gdi1X.n6-42
Source: [PDB-id:chain] 2gdi:X (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THIAMINE PYROPHOSPHATE-SPECIFIC RIBOSWITCH IN COMPLEX WITH THIAMINE PYROPHOSPHATE
Source: Compound TPP RIBOSWITCH
Source: Resolution 2.05 ANGSTROMS.
Position (9, 39), (12, 29)
Primary structure ('_': anchors) _GU_-_UGAGAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-exo, 10: C1'-exo, 11: C2'-endo, 12: C2'-exo, 13: C1'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		10: syn, 12: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 11 ↑
4 4 10 ↓
5 5 6 ↑
6 6 7 ↑
7 8 9 ↑
8 12 14 ↑
9 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 2 9 Sugar/Sugar trans
3 2 14 Watson-Crick/Watson-Crick cis
4 3 12 Watson-Crick/Watson-Crick cis
5 4 5 Watson-Crick/Watson-Crick cis
6 6 10 Hoogsteen/Watson-Crick trans
7 7 9 Hoogsteen/O2' ?
8 7 10 O2'/Watson-Crick ?
9 8 15 O2'/Sugar ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters