Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-15-45-Multiloop pdb1p9x10.m43-374
Source: [PDB-id:chain] 1p9x:0 (&rarr PDB)
Source: Information THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTIC
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.40 ANGSTROMS.
Position (44, 373), (45, 156), (161, 189), (201, 208), (212, 239), (255, 327)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAAGAAA_-_GAU_-_UCAGCCCAAAUUCGA_-_GUAAGGUCGUUGUUCGUGAACGCGCAAGGCUAAAUAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		20: C4'-exo, 31: C2'-exo, 49: C2'-exo, 50: C2'-exo, 51: C2'-exo, 54: C4'-exo, 65: C2'-exo, 72: C4'-exo, 73: C4'-exo, 74: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		20: syn, 51: syn
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 11 12 ↑
7 13 80 →
8 15 16 ↑
9 16 17 ↑
10 17 75 &larr
11 18 24 →
12 19 21 ↑
13 24 25 ↑
14 25 26 ↑
15 27 28 ↑
16 28 29 ↑
17 32 33 ↑
18 33 34 ↑
19 34 35 ↑
20 37 38 ↑
21 39 40 ↑
22 39 42 →
23 42 43 ↑
24 43 44 ↑
25 48 49 ↑
26 54 55 ↑
27 56 57 ↑
28 57 59 &larr
29 58 59 ↑
30 72 73 ↑
31 74 75 ↑
32 76 77 ↑
33 80 81 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 81 Watson-Crick/Watson-Crick cis
2 2 3 Watson-Crick/Watson-Crick cis
3 4 5 Hoogsteen/O2' ?
4 7 11 Watson-Crick/Watson-Crick cis
5 7 80 Sugar/O2' ?
6 8 9 Watson-Crick/Watson-Crick cis
7 11 13 O2'/Sugar ?
8 17 24 Sugar/O2' ?
9 17 76 O2'/Bifurcated ?
10 18 73 C/O2' ?
11 18 74 Hoogsteen/Hoogsteen cis y
12 19 22 Watson-Crick/Watson-Crick cis y
13 19 32 Bifurcated/O2' ?
14 20 67 Watson-Crick/O2' ?
15 21 22 Watson-Crick/Watson-Crick cis y
16 21 67 O2'/Hoogsteen ?
17 25 78 Watson-Crick/Watson-Crick trans y
18 26 27 Watson-Crick/Watson-Crick cis
19 27 78 O2'/Sugar ?
20 31 32 O2'/Watson-Crick ?
21 32 73 Watson-Crick/Watson-Crick cis y
22 34 47 Sugar/Hoogsteen cis y
23 37 43 Watson-Crick/Watson-Crick trans y
24 38 42 Watson-Crick/Hoogsteen cis y
25 40 41 Watson-Crick/Watson-Crick cis
26 49 71 Bifurcated/O2' ?
27 50 51 Sugar/C trans y
28 57 59 Bifurcated/O2' ?
29 57 63 Hoogsteen/Sugar trans y
30 60 62 Bifurcated/O2' ?
31 61 62 Hoogsteen/O2' ?
32 66 68 Watson-Crick/Hoogsteen cis y
33 67 69 Hoogsteen/Watson-Crick cis y
34 68 69 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters