Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb1vsp1w.m43-462
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 (44, 461), (45, 169), (174, 202), (214, 221), (225, 252), (256, 454)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAGGAAA_-_GAC_-_CCA_-_UAAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C4'-exo, 6: C2'-exo, 9: C2'-exo, 12: C4'-exo, 19: C3'-exo, 23: C2'-endo, 24: C2'-exo, 30: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		30: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 4 ↑
2 5 6 ↑
3 6 7 ↑
4 9 10 ↑
5 11 12 ↑
6 13 14 ↑
7 13 38 →
8 14 15 ↑
9 15 16 ↑
10 16 17 ↑
11 17 33 &larr
12 18 24 →
13 18 31 ↑
14 19 21 ↑
15 22 23 ↑
16 24 25 ↑
17 25 26 ↑
18 27 28 ↑
19 28 29 ↑
20 30 34 →
21 32 33 ↑
22 34 35 ↑
23 38 39 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 5 Watson-Crick/Sugar trans y
2 1 39 Watson-Crick/Watson-Crick cis
3 2 3 Watson-Crick/Watson-Crick cis
4 4 5 Hoogsteen/O2' ?
5 4 11 Hoogsteen/Watson-Crick trans y
6 6 39 O2'/Sugar ?
7 7 11 Watson-Crick/Watson-Crick cis
8 7 38 Sugar/O2' ?
9 8 9 Watson-Crick/Watson-Crick cis
10 8 14 Sugar/O2' ?
11 11 13 Sugar/Sugar cis y
12 12 38 Bifurcated/O2' trans y
13 13 37 Watson-Crick/Hoogsteen trans
14 16 34 O2'/Watson-Crick ?
15 17 18 C/O2' ?
16 17 34 O2'/Watson-Crick trans y
17 18 30 O2'/Watson-Crick ?
18 18 33 Watson-Crick/Hoogsteen trans
19 21 22 Watson-Crick/Watson-Crick cis
20 24 35 Watson-Crick/Watson-Crick trans
21 25 36 Watson-Crick/Watson-Crick trans
22 26 27 Watson-Crick/Watson-Crick cis
23 27 36 O2'/Sugar ?
24 28 35 Sugar/O2' ?
25 30 34 Bifurcated/O2' ?
26 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters