Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-6-5-6-2-Multiloop pdb3d5b1A.m251-449
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 (253, 447), (258, 278), (285, 392), (398, 422), (429, 444)
Primary structure ('_': anchors) _UAAA_-_GGUCGU_-_GAGUA_-_GAAUCU_-_AA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C4'-exo, 10: C1'-exo, 12: C2'-endo, 16: C2'-endo, 17: C2'-endo, 18: C1'-exo, 24: C4'-exo, 26: C2'-endo, 27: C2'-endo, 28: C2'-endo, 30: C3'-exo, 33: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		28: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 10 &larr
3 3 4 ↑
4 3 16 →
5 4 5 ↑
6 7 8 ↑
7 8 9 ↑
8 9 10 ↑
9 12 14 →
10 12 30 &larr
11 14 27 ↓
12 16 33 ↑
13 17 19 →
14 18 23 &larr
15 19 20 ↑
16 20 21 ↑
17 20 24 →
18 22 23 ↑
19 24 25 ↑
20 25 26 ↑
21 27 29 →
22 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
3 3 9 Bifurcated/O2' ?
4 3 10 Watson-Crick/Hoogsteen trans
5 5 6 Bifurcated/O2' ?
6 6 7 Watson-Crick/Watson-Crick cis
7 11 14 Sugar/Bifurcated cis y
8 12 27 Watson-Crick/Watson-Crick cis
9 14 15 Watson-Crick/Watson-Crick cis
10 15 27 O2'/Bifurcated ?
11 16 26 Watson-Crick/O2' ?
12 16 32 Bifurcated/O2' ?
13 17 25 O2'/Bifurcated trans y
14 18 19 Hoogsteen/Sugar cis y
15 18 24 O2'/Bifurcated ?
16 19 23 Watson-Crick/O2' ?
17 19 24 Hoogsteen/Watson-Crick trans
18 20 23 Sugar/Hoogsteen trans y
19 21 22 Watson-Crick/Watson-Crick cis
20 25 32 Watson-Crick/Watson-Crick trans y
21 29 30 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters