Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-0-3-21-0-4-Multiloop pdb1yl31A.m837-1219
Source: [PDB-id:chain] 1yl3:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF 70S RIBOSOME WITH THRS OPERATOR AND TRNAS. LARGE SUBUNIT. THE COORDINATES FOR THE SMALL SUBUNIT ARE IN THE PDB ENTRY 1YL4.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 5.50 ANGSTROMS.
Position (842, 1214), (847, 860), (861, 966), (970, 993), (1015, 1188), (1189, 1209)
Primary structure ('_': anchors) _GAAA_-__-_GAG_-_CGAGCGCGGGAACAACCGAGA_-__-_GGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 6: C4'-exo, 10: C2'-exo, 11: C4'-exo, 15: C4'-exo, 18: C4'-exo, 20: C2'-exo, 21: C4'-exo, 22: C4'-exo, 25: C4'-exo, 27: C4'-exo, 28: C4'-exo, 30: C2'-exo, 31: C2'-exo, 38: C4'-exo, 40: C2'-exo, 41: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		17: syn, 28: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 3 43 →
4 7 8 ↑
5 12 13 ↑
6 20 35 →
7 22 23 ↑
8 22 32 →
9 23 24 ↑
10 24 27 &larr
11 25 26 ↑
12 32 33 ↑
13 36 38 →
14 43 44 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 44 Watson-Crick/Watson-Crick cis
2 2 42 O2'/Watson-Crick ?
3 3 9 Sugar/Bifurcated trans y
4 3 41 Bifurcated/O2' ?
5 3 42 Watson-Crick/Bifurcated trans y
6 4 8 Bifurcated/O2' ?
7 4 10 O2'/Sugar ?
8 4 16 Watson-Crick/O2' ?
9 6 7 Watson-Crick/Watson-Crick cis y
10 8 9 Watson-Crick/Watson-Crick cis y
11 9 10 Hoogsteen/Hoogsteen trans y
12 12 15 Hoogsteen/Watson-Crick cis y
13 13 14 Watson-Crick/Watson-Crick cis
14 14 15 Hoogsteen/Watson-Crick cis y
15 16 18 O2'/Hoogsteen ?
16 18 28 O2'/Bifurcated ?
17 18 42 Hoogsteen/O2' ?
18 19 34 Bifurcated/O2' ?
19 19 40 Bifurcated/O2' cis y
20 21 32 Watson-Crick/Watson-Crick cis
21 23 30 Watson-Crick/Watson-Crick cis
22 24 26 O2'/Hoogsteen ?
23 26 27 Bifurcated/O2' ?
24 28 29 O2'/Hoogsteen ?
25 35 40 O2'/Watson-Crick trans y
26 36 37 Watson-Crick/Watson-Crick cis
27 38 39 Watson-Crick/Watson-Crick cis
28 43 44 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters