Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-5-6-2-Multiloop pdb2j011A.m248-442
Source: [PDB-id:chain] 2j01:A (&rarr PDB)
Source: Information STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 2 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT FROM MOLECULE I.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.80 ANGSTROMS.
Position (250, 440), (255, 275), (281, 385), (391, 415), (422, 437)
Primary structure ('_': anchors) _UAAA_-_GGUCG_-_GAGUA_-_GAAUCU_-_AA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		10: C2'-endo, 12: C3'-exo, 15: C2'-endo, 16: C2'-endo, 17: C2'-endo, 25: C2'-endo, 26: C2'-endo, 27: C2'-endo, 29: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		27: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 10 &larr
3 3 4 ↑
4 3 15 →
5 4 5 ↑
6 7 8 ↑
7 8 9 ↑
8 12 13 →
9 12 29 &larr
10 13 26 ↓
11 15 32 ↑
12 16 18 →
13 17 22 &larr
14 19 20 ↑
15 19 23 →
16 21 22 ↑
17 23 24 ↑
18 24 25 ↑
19 26 28 →
20 30 31 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 32 Watson-Crick/Watson-Crick cis
2 2 15 Watson-Crick/Watson-Crick cis
3 3 9 Bifurcated/O2' ?
4 3 10 Watson-Crick/Hoogsteen trans
5 3 14 O2'/Bifurcated ?
6 4 9 O2'/Bifurcated trans
7 5 8 Sugar/Hoogsteen trans y
8 6 7 Watson-Crick/Watson-Crick cis y
9 12 26 Watson-Crick/Watson-Crick cis
10 13 14 Watson-Crick/Watson-Crick cis
11 15 25 Watson-Crick/O2' ?
12 16 24 Hoogsteen/Hoogsteen trans
13 17 18 Hoogsteen/Sugar cis y
14 17 23 O2'/Bifurcated ?
15 18 22 Watson-Crick/O2' ?
16 18 23 Hoogsteen/Watson-Crick trans
17 18 31 Sugar/O2' ?
18 19 20 Bifurcated/O2' ?
19 19 22 O2'/Bifurcated trans
20 20 21 Watson-Crick/Watson-Crick cis
21 24 31 Watson-Crick/Watson-Crick trans y
22 28 29 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters