Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-6-5-6-2-Multiloop pdb1vsp1w.m256-454
Source: [PDB-id:chain] 1vsp:w (&rarr PDB)
Source: Information INTERACTIONS AND DYNAMICS OF THE SHINE-DALGARNO HELIX IN THE 70S RIBOSOME. THIS FILE, 1VSP, CONTAINS THE 50S RIBOSOME SUBUNIT. 30S RIBOSOME SUBUNIT IS IN THE FILE 2QNH
Source: Compound 23S LARGE SUBUNIT RIBOSOMAL RNA
Source: Resolution 3.83 ANGSTROMS.
Position (258, 452), (263, 283), (290, 397), (403, 427), (434, 449)
Primary structure ('_': anchors) _UAAA_-_GGUCGU_-_GAGUA_-_GAAUCU_-_AA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-exo, 2: C2'-exo, 6: C2'-exo, 12: O4'-endo, 14: C2'-exo, 15: C2'-exo, 16: C4'-exo, 18: C4'-exo, 26: C4'-exo, 27: C4'-exo, 28: C2'-exo, 30: C3'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 10 &larr
2 3 4 ↑
3 3 16 →
4 7 8 ↑
5 8 9 ↑
6 12 30 &larr
7 14 27 ↓
8 16 33 ↑
9 17 19 →
10 18 23 &larr
11 20 21 ↑
12 20 24 →
13 22 23 ↑
14 24 25 ↑
15 27 29 →
16 31 32 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 33 Watson-Crick/Watson-Crick cis
2 2 16 Watson-Crick/Watson-Crick cis y
3 3 9 Bifurcated/O2' ?
4 3 10 Watson-Crick/Hoogsteen trans
5 4 9 O2'/Bifurcated trans y
6 5 8 O2'/Bifurcated trans y
7 6 7 Watson-Crick/Watson-Crick cis
8 11 12 Hoogsteen/O2' ?
9 12 27 Watson-Crick/Watson-Crick cis
10 13 14 O2'/Watson-Crick ?
11 14 15 Watson-Crick/Watson-Crick cis
12 15 26 Watson-Crick/O2' ?
13 15 27 O2'/Bifurcated ?
14 17 25 Hoogsteen/Hoogsteen trans
15 17 32 Sugar/O2' ?
16 18 23 Watson-Crick/O2' ?
17 18 24 O2'/Bifurcated ?
18 19 23 Bifurcated/O2' ?
19 19 24 Hoogsteen/Watson-Crick trans
20 19 32 Sugar/O2' ?
21 20 23 Sugar/Hoogsteen trans
22 21 22 Watson-Crick/Watson-Crick cis
23 29 30 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters