Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb2j011A.m38-450
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 (39, 449), (40, 161), (166, 194), (206, 213), (217, 244), (248, 442)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAGGAAA_-_GAC_-_CCA_-_UAAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		12: C2'-endo, 19: C2'-endo, 23: C2'-endo, 30: C2'-endo
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 25 26 ↑
19 27 28 ↑
20 28 29 ↑
21 30 34 →
22 32 33 ↑
23 34 35 ↑
24 35 36 ↑
25 38 39 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 39 Watson-Crick/Watson-Crick cis
2 2 3 Watson-Crick/Watson-Crick cis
3 4 5 Hoogsteen/O2' ?
4 4 11 Hoogsteen/Watson-Crick trans y
5 4 12 Hoogsteen/Sugar trans y
6 6 12 Watson-Crick/Watson-Crick cis
7 6 39 O2'/Sugar cis y
8 7 11 Watson-Crick/Watson-Crick cis
9 7 38 Sugar/O2' cis y
10 8 9 Watson-Crick/Watson-Crick cis
11 8 14 Sugar/O2' ?
12 11 13 O2'/Sugar cis y
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' cis y
18 17 34 O2'/Watson-Crick trans y
19 18 30 O2'/Watson-Crick ?
20 18 33 Watson-Crick/Hoogsteen trans
21 19 23 Sugar/Hoogsteen trans
22 21 22 Watson-Crick/Watson-Crick cis
23 24 35 Watson-Crick/Watson-Crick trans
24 25 36 Watson-Crick/Watson-Crick trans
25 26 27 Watson-Crick/Watson-Crick cis
26 27 36 O2'/Sugar cis y
27 28 35 Sugar/O2' ?
28 30 33 O2'/Bifurcated ?
29 30 34 Bifurcated/O2' ?
30 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters