Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-5-5-6-Multiloop pdb2ogn10.m43-397
Source: [PDB-id:chain] 2ogn:0 (&rarr PDB)
Source: Information THE CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH THE PLEUROMUTILIN DERIVATIVE SB-280080
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.56 ANGSTROMS.
Position (44, 396), (45, 156), (161, 189), (201, 208), (214, 237), (243, 389)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAAGAAA_-_GAUUC_-_GAUCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		10: C4'-exo, 18: C4'-exo, 19: C4'-exo, 20: C4'-exo, 24: C2'-exo, 38: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		19: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 4 ↑
2 5 6 ↑
3 9 10 ↑
4 10 11 ↑
5 11 12 ↑
6 13 14 ↑
7 13 42 →
8 14 15 ↑
9 15 16 ↑
10 16 17 ↑
11 17 37 &larr
12 18 24 →
13 18 35 ↑
14 25 26 ↑
15 26 27 ↑
16 29 30 ↑
17 31 32 ↑
18 32 33 ↑
19 36 37 ↑
20 39 40 ↑
21 42 43 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 43 Watson-Crick/Watson-Crick cis
2 2 3 Watson-Crick/Watson-Crick cis
3 4 5 Hoogsteen/O2' ?
4 6 12 Watson-Crick/Watson-Crick cis y
5 6 43 O2'/Sugar ?
6 7 11 Watson-Crick/Watson-Crick cis
7 7 42 Sugar/O2' ?
8 8 9 Watson-Crick/Watson-Crick cis
9 11 13 O2'/Sugar ?
10 12 42 Watson-Crick/Sugar trans y
11 17 24 Sugar/O2' ?
12 17 38 O2'/Bifurcated ?
13 18 35 O2'/Watson-Crick ?
14 19 23 O2'/Watson-Crick ?
15 21 22 Watson-Crick/Watson-Crick cis
16 25 40 Watson-Crick/Watson-Crick trans y
17 26 31 Watson-Crick/Watson-Crick cis
18 27 30 Bifurcated/Watson-Crick cis
19 28 29 Watson-Crick/Watson-Crick cis
20 31 40 O2'/Sugar ?
21 32 39 Sugar/O2' ?
22 35 36 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters