Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'2-9-Internal Loop pdb3d2g1B.n13-26
Source: [PDB-id:chain] 3d2g:B (&rarr PDB)
Source: Information STRUCTURAL BASIS OF THIAMINE PYROPHOSPHATE ANALOGUES BINDING TO THE EUKARYOTIC RIBOSWITCH
Source: Compound TPP-SPECIFIC RIBOSWITCH
Source: Resolution 2.25 ANGSTROMS.
Position (10, 36), (13, 26)
Primary structure ('_': anchors) _GU_-_UGAGAAAGU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C4'-exo, 5: C2'-exo, 10: C1'-exo, 11: C2'-endo, 12: C2'-exo, 13: C2'-exo, 14: C1'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		11: syn, 12: syn, 14: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 11 &larr
4 4 10 ↓
5 5 6 ↑
6 6 7 ↑
7 8 9 ↑
8 12 13 ↓
9 13 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 13 Bifurcated/Watson-Crick cis
4 3 12 Hoogsteen/Watson-Crick cis
5 4 5 Watson-Crick/Watson-Crick cis
6 4 10 O2'/Hoogsteen ?
7 6 10 Hoogsteen/Watson-Crick trans
8 7 9 Hoogsteen/O2' ?
9 7 10 O2'/Watson-Crick ?
10 8 15 O2'/Sugar ?
11 9 13 Hoogsteen/O2' ?
12 12 13 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters