Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb3d5b1A.m38-457
Source: [PDB-id:chain] 3d5b:A (&rarr PDB)
Source: Information STRUCTURAL BASIS FOR TRANSLATION TERMINATION ON THE 70S RIBOSOME. THIS FILE CONTAINS THE 50S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AS DESCRIBED IN REMARK 400.
Source: Compound 23S RRNA
Source: Resolution 3.21 ANGSTROMS.
Position (39, 456), (40, 164), (169, 197), (209, 216), (220, 247), (251, 449)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAGGAAA_-_GAC_-_CCA_-_UAAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-exo, 12: C2'-endo, 18: C2'-exo, 19: C2'-endo, 23: C2'-endo, 30: C2'-endo, 34: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		19: syn, 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 10 11 ↑
6 11 12 ↑
7 13 14 ↑
8 13 38 →
9 14 15 ↑
10 15 16 ↑
11 16 17 ↑
12 17 33 &larr
13 18 24 →
14 18 31 ↑
15 19 21 ↑
16 22 23 ↑
17 24 25 ↑
18 27 28 ↑
19 28 29 ↑
20 30 34 →
21 34 35 ↑
22 35 36 ↑
23 38 39 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 12 O2'/Hoogsteen ?
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 12 Watson-Crick/Watson-Crick cis
7 6 39 O2'/Sugar ?
8 7 11 Watson-Crick/Watson-Crick cis
9 7 38 Sugar/O2' ?
10 8 9 Watson-Crick/Watson-Crick cis
11 8 14 Sugar/O2' ?
12 11 13 O2'/Sugar ?
13 12 38 Watson-Crick/Sugar trans y
14 13 37 Watson-Crick/Hoogsteen trans
15 16 25 O2'/Sugar cis y
16 16 36 Watson-Crick/Watson-Crick cis y
17 17 24 Sugar/O2' ?
18 17 34 O2'/Bifurcated ?
19 18 30 O2'/Watson-Crick ?
20 18 33 Watson-Crick/Hoogsteen trans
21 21 22 Watson-Crick/Watson-Crick cis
22 25 36 Watson-Crick/Watson-Crick trans
23 26 27 Watson-Crick/Watson-Crick cis
24 27 36 O2'/Sugar ?
25 28 35 Sugar/O2' ?
26 28 36 Sugar/Watson-Crick cis y
27 29 34 Watson-Crick/O2' ?
28 30 33 O2'/Bifurcated ?
29 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters