Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb1y6910.m43-397
Source: [PDB-id:chain] 1y69:0 (&rarr PDB)
Source: Information RRF DOMAIN I IN COMPLEX WITH THE 50S RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.33 ANGSTROMS.
Position (44, 396), (45, 156), (161, 189), (201, 208), (212, 239), (243, 389)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAAGAAA_-_GAU_-_UCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-exo, 15: C2'-exo, 19: C4'-exo, 23: C2'-exo, 24: C2'-exo, 34: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
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 13 14 ↑
7 13 38 →
8 14 15 ↑
9 15 16 ↑
10 16 17 ↑
11 17 33 &larr
12 18 24 →
13 18 31 ↑
14 19 21 ↑
15 22 23 ↑
16 27 28 ↑
17 28 29 ↑
18 32 33 ↑
19 34 35 ↑
20 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 12 Watson-Crick/Bifurcated trans y
5 5 12 Watson-Crick/Bifurcated cis y
6 6 12 Watson-Crick/Watson-Crick cis y
7 7 11 Watson-Crick/Watson-Crick cis
8 7 13 Watson-Crick/O2' ?
9 7 38 Sugar/O2' ?
10 8 9 Watson-Crick/Watson-Crick cis
11 11 13 O2'/Sugar ?
12 13 37 Watson-Crick/Hoogsteen trans
13 16 25 O2'/Sugar ?
14 16 34 O2'/Bifurcated ?
15 17 24 Sugar/O2' ?
16 17 34 O2'/Bifurcated ?
17 18 31 O2'/Watson-Crick ?
18 19 23 Sugar/Watson-Crick trans y
19 21 22 Watson-Crick/Watson-Crick cis
20 25 36 Watson-Crick/Watson-Crick trans y
21 26 27 Watson-Crick/Watson-Crick cis
22 27 36 O2'/Sugar ?
23 30 33 O2'/Watson-Crick ?
24 30 34 Hoogsteen/Hoogsteen trans
25 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters