Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb3cf51X.m43-375
Source: [PDB-id:chain] 3cf5:X (&rarr PDB)
Source: Information THIOPEPTIDE ANTIBIOTIC THIOSTREPTON BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS
Source: Compound RRNA-23S RIBOSOMAL RNA
Source: Resolution 3.30 ANGSTROMS.
Position (44, 374), (45, 156), (161, 189), (201, 208), (212, 239), (243, 367)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAAGAAA_-_GAU_-_UCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		10: C4'-exo, 12: C4'-exo, 18: C4'-exo, 19: O4'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 4 →
2 3 4 ↑
3 5 6 ↑
4 6 7 ↑
5 9 10 ↑
6 10 11 ↑
7 11 12 ↑
8 13 14 ↑
9 13 38 →
10 14 15 ↑
11 15 16 ↑
12 16 17 ↑
13 17 33 &larr
14 18 24 →
15 18 31 ↑
16 19 21 ↑
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 12 Hoogsteen/O2' ?
2 1 39 Watson-Crick/Watson-Crick cis
3 2 3 Watson-Crick/Watson-Crick cis
4 4 5 Hoogsteen/O2' ?
5 4 11 Hoogsteen/Watson-Crick trans y
6 6 12 Watson-Crick/Watson-Crick cis
7 6 39 O2'/Sugar ?
8 7 11 Watson-Crick/Watson-Crick cis
9 7 13 Watson-Crick/O2' ?
10 7 38 Sugar/O2' cis y
11 8 9 Watson-Crick/Watson-Crick cis
12 11 13 O2'/Sugar cis y
13 12 38 Watson-Crick/Sugar trans y
14 13 37 Watson-Crick/Hoogsteen trans y
15 16 25 O2'/Sugar cis y
16 17 24 Sugar/O2' cis
17 17 34 O2'/Watson-Crick ?
18 18 33 Watson-Crick/Hoogsteen trans
19 21 22 Watson-Crick/Watson-Crick cis
20 25 36 Watson-Crick/Watson-Crick trans
21 26 27 Watson-Crick/Watson-Crick cis
22 27 36 O2'/Sugar ?
23 28 35 Sugar/O2' ?
24 30 33 O2'/Bifurcated ?
25 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters