Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'20-5-4-3-3-7-Multiloop pdb1pny10.m775-1159
Source: [PDB-id:chain] 1pny:0 (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE WILD TYPE RIBOSOME FROM E. COLI, 50S SUBUNIT OF 70S RIBOSOME. THIS FILE, 1PNY, CONTAINS ONLY MOLECULES OF THE 50S RIBOSOMAL SUBUNIT. THE 30S SUBUNIT IS IN THE PDB FILE 1PNX.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 9.50 ANGSTROMS.
Position (780, 1154), (801, 901), (907, 932), (937, 948), (952, 1124), (1128, 1146)
Primary structure ('_': anchors) _GAAAUGUAUUGAGGUACAGC_-_AGUGA_-_GAGA_-_AGA_-_AUU_-_UCUGGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		None
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		12: syn, 33: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 51 &larr
3 3 4 ↑
4 3 53 →
5 4 5 ↑
6 5 29 ↑
7 7 8 ↑
8 8 9 ↑
9 9 10 ↑
10 15 16 ↑
11 17 18 ↑
12 18 19 ↑
13 19 20 ↑
14 20 21 ↑
15 22 24 →
16 24 25 ↑
17 25 26 ↑
18 26 27 ↑
19 30 31 ↑
20 33 50 ↑
21 34 35 ↑
22 36 37 ↑
23 41 42 ↑
24 42 43 ↑
25 43 44 ↑
26 46 47 ↑
27 47 48 ↑
28 50 51 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 54 Watson-Crick/Watson-Crick cis
2 2 52 O2'/Watson-Crick ?
3 3 25 O2'/Watson-Crick ?
4 3 51 Watson-Crick/O2' ?
5 4 26 O2'/Sugar ?
6 4 32 O2'/Bifurcated ?
7 5 27 O2'/Sugar ?
8 5 31 O2'/Bifurcated trans y
9 6 29 Hoogsteen/O2' ?
10 7 18 Watson-Crick/Watson-Crick cis
11 10 15 Watson-Crick/Watson-Crick cis
12 11 12 Bifurcated/O2' ?
13 16 27 Hoogsteen/O2' ?
14 17 27 Watson-Crick/O2' ?
15 21 25 Watson-Crick/Watson-Crick cis
16 22 23 Watson-Crick/Watson-Crick cis
17 25 53 Sugar/O2' ?
18 29 30 Watson-Crick/Watson-Crick cis
19 30 33 Bifurcated/O2' ?
20 30 38 Bifurcated/O2' ?
21 31 33 Bifurcated/O2' ?
22 32 50 Bifurcated/O2' cis y
23 34 38 O2'/Bifurcated ?
24 35 36 Watson-Crick/Watson-Crick cis
25 39 50 O2'/Hoogsteen ?
26 40 41 Watson-Crick/Watson-Crick cis
27 45 46 Watson-Crick/Watson-Crick cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters