Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'23-Segment pdb1j2b1D.i40-64
Source: [PDB-id:chain] 1j2b:D (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF ARCHAEOSINE TRNA-GUANINE TRANSGLYCOSYLASE COMPLEXED WITH LAMBDA-FORM TRNA(VAL)
Source: Compound TRNA(VAL)
Source: Resolution 3.30 ANGSTROMS.
Position (40, 64)
Primary structure ('_': anchors) _GAGGUCCGGGGUUCAAGUCCCCG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-exo, 7: C4'-exo, 16: C4'-exo, 19: C4'-exo, 25: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		18: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 5 6 ↑
5 6 7 ↑
6 9 10 ↑
7 9 24 →
8 10 11 ↑
9 11 12 ↑
10 12 13 ↑
11 13 14 ↑
12 18 19 →
13 22 23 ↑
14 23 24 ↑
15 24 25 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 4 5 Hoogsteen/O2' ?
2 8 24 Watson-Crick/Watson-Crick cis
3 10 22 Watson-Crick/Watson-Crick cis y
4 12 20 Watson-Crick/Watson-Crick cis y
5 12 21 Watson-Crick/Watson-Crick cis
6 14 17 O2'/Watson-Crick ?
7 19 20 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters