Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'20-5-4-3-3-7-Multiloop pdb1njn10.m775-1143
Source: [PDB-id:chain] 1njn:0 (&rarr PDB)
Source: Information THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH THE ANTIBIOTIC SPARSOMYCIN
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.70 ANGSTROMS.
Position (780, 1138), (801, 885), (891, 916), (921, 932), (936, 1108), (1112, 1130)
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 6 7 ↑
8 7 8 ↑
9 8 9 ↑
10 9 10 ↑
11 15 16 ↑
12 16 27 &larr
13 17 18 ↑
14 18 19 ↑
15 19 20 ↑
16 20 21 ↑
17 22 24 →
18 24 25 ↑
19 25 26 ↑
20 26 27 ↑
21 30 31 ↑
22 32 52 →
23 33 50 ↑
24 34 35 ↑
25 36 37 ↑
26 41 42 ↑
27 42 43 ↑
28 43 44 ↑
29 46 47 ↑
30 47 48 ↑
31 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 3 52 Watson-Crick/Hoogsteen trans y
6 4 26 O2'/Sugar ?
7 4 32 O2'/Bifurcated ?
8 5 27 O2'/Sugar ?
9 5 31 O2'/Bifurcated trans
10 6 29 Hoogsteen/O2' ?
11 7 18 Watson-Crick/Watson-Crick cis y
12 10 15 Watson-Crick/Watson-Crick cis
13 11 12 Hoogsteen/O2' ?
14 16 27 Hoogsteen/O2' ?
15 17 27 Watson-Crick/O2' ?
16 21 25 Watson-Crick/Watson-Crick cis
17 22 23 Watson-Crick/Watson-Crick cis
18 25 53 Sugar/O2' ?
19 29 30 Watson-Crick/Watson-Crick cis
20 30 33 Bifurcated/O2' ?
21 30 38 Bifurcated/O2' ?
22 31 33 Bifurcated/O2' ?
23 32 50 Bifurcated/O2' ?
24 34 38 O2'/Bifurcated ?
25 35 36 Watson-Crick/Watson-Crick cis
26 40 41 Watson-Crick/Watson-Crick cis
27 45 46 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters