Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb2ogo10.m42-396
Source: [PDB-id:chain] 2ogo:0 (&rarr PDB)
Source: Information THE CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH THE PLEUROMUTILIN DERIVATIVE RETAPAMULIN (SB-275833)
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.66 ANGSTROMS.
Position (43, 395), (44, 155), (160, 188), (200, 207), (211, 238), (242, 388)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAAGAAA_-_GAU_-_UCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-exo, 10: C4'-exo, 18: C4'-exo, 19: O4'-endo, 24: C2'-exo, 34: C4'-exo, 36: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 12 &larr
2 3 4 ↑
3 5 6 ↑
4 6 7 ↑
5 9 10 ↑
6 10 11 ↑
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 27 28 ↑
18 28 29 ↑
19 32 33 ↑
20 35 36 ↑
21 38 39 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 12 Hoogsteen/O2' ?
2 1 39 Watson-Crick/Watson-Crick cis
3 2 3 Watson-Crick/Watson-Crick cis
4 2 11 O2'/Bifurcated ?
5 6 39 O2'/Sugar ?
6 7 11 Watson-Crick/Watson-Crick cis
7 7 38 Sugar/O2' ?
8 8 9 Watson-Crick/Watson-Crick cis
9 11 13 O2'/Sugar ?
10 15 26 O2'/Watson-Crick ?
11 16 25 O2'/Sugar ?
12 17 24 Sugar/O2' ?
13 17 34 O2'/Bifurcated ?
14 18 33 Watson-Crick/Hoogsteen trans y
15 19 23 Sugar/Hoogsteen trans y
16 21 22 Watson-Crick/Watson-Crick cis
17 25 36 Watson-Crick/Watson-Crick trans y
18 26 27 Watson-Crick/Watson-Crick cis
19 27 36 O2'/Sugar cis y
20 28 35 Sugar/O2' ?
21 30 33 O2'/Watson-Crick ?
22 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters