Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb1vsa1w.n225-252
Source: [PDB-id:chain] 1vsa:w (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF A 70S RIBOSOME-TRNA COMPLEX REVEALS FUNCTIONAL INTERACTIONS AND REARRANGEMENTS. THIS FILE, 1VSA, CONTAINS THE 50S RIBOSOME SUBUNIT. 30S RIBOSOME SUBUNIT IS IN THE FILE 2OW8
Source: Compound 23S LARGE SUBUNIT RIBOSOMAL RNA
Source: Resolution 3.71 ANGSTROMS.
Position (229, 248), (235, 243)
Primary structure ('_': anchors) _GAGUA_-_GAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C4'-exo, 4: C4'-exo, 12: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 &larr
3 3 5 →
4 4 9 &larr
5 6 7 ↑
6 6 10 →
7 8 9 ↑
8 10 11 ↑
9 11 12 ↑
10 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis y
2 2 12 Bifurcated/O2' trans
3 3 11 O2'/Bifurcated ?
4 4 9 Watson-Crick/O2' ?
5 4 10 O2'/Bifurcated ?
6 5 10 Hoogsteen/Watson-Crick trans
7 6 9 O2'/Bifurcated trans
8 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters