Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-2-2-2-8-Multiloop pdb3d5d1A.m598-1281
Source: [PDB-id:chain] 3d5d:A (&rarr PDB)
Source: Information STRUCTURAL BASIS FOR TRANSLATION TERMINATION ON THE 70S RIBOSOME. THIS FILE CONTAINS THE 50S SUBUNIT OF THE SECOND 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 (603, 1276), (608, 689), (692, 830), (833, 1214), (1217, 1267)
Primary structure ('_': anchors) _GACU_-_GA_-_UU_-_CG_-_GUGCGAAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 4: C2'-endo, 7: C2'-exo, 8: C3'-exo, 9: C2'-endo, 13: C2'-endo, 19: C2'-endo, 20: C2'-endo, 22: C2'-endo, 23: C2'-endo, 24: C2'-endo, 25: C1'-exo, 26: C4'-exo, 27: C4'-exo, 28: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		24: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 23 &larr
3 3 26 →
4 5 6 ↑
5 7 9 &larr
6 11 12 ↑
7 14 22 ↓
8 15 16 ↑
9 16 17 ↑
10 17 18 ↑
11 17 22 →
12 19 21 ↑
13 24 25 ↑
14 26 28 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 28 Watson-Crick/Watson-Crick cis
2 2 25 O2'/Watson-Crick ?
3 2 26 Hoogsteen/Sugar trans
4 3 11 O2'/Watson-Crick trans y
5 3 23 Watson-Crick/Hoogsteen trans y
6 5 9 Sugar/Watson-Crick trans y
7 6 7 Watson-Crick/Watson-Crick cis
8 10 11 Watson-Crick/Watson-Crick cis
9 12 25 Hoogsteen/O2' ?
10 13 22 O2'/Watson-Crick ?
11 14 15 Watson-Crick/Watson-Crick cis
12 17 21 Bifurcated/Watson-Crick cis y
13 18 19 Watson-Crick/Watson-Crick cis
14 24 25 Hoogsteen/O2' ?
15 26 28 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters