Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb2zjp1X.m43-375
Source: [PDB-id:chain] 2zjp:X (&rarr PDB)
Source: Information THIOPEPTIDE ANTIBIOTIC NOSIHEPTIDE BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS
Source: Compound RIBOSOMAL 23S RNA
Source: Resolution 3.70 ANGSTROMS.
Position (44, 374), (45, 156), (161, 189), (201, 208), (212, 239), (243, 367)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAAGAAA_-_GAU_-_UCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		19: C4'-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 11 12 ↑
7 13 14 ↑
8 13 38 →
9 14 15 ↑
10 15 16 ↑
11 16 17 ↑
12 17 33 &larr
13 18 24 →
14 18 31 ↑
15 19 21 ↑
16 24 25 ↑
17 25 26 ↑
18 27 28 ↑
19 28 29 ↑
20 30 34 →
21 32 33 ↑
22 35 36 ↑
23 38 39 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 39 Watson-Crick/Watson-Crick cis
2 2 3 Watson-Crick/Watson-Crick cis
3 4 5 Hoogsteen/O2' ?
4 4 11 Hoogsteen/Watson-Crick trans y
5 4 12 Hoogsteen/Sugar trans y
6 6 12 Watson-Crick/Watson-Crick cis
7 6 39 O2'/Sugar ?
8 7 11 Watson-Crick/Watson-Crick cis
9 7 38 Sugar/O2' cis y
10 8 9 Watson-Crick/Watson-Crick cis
11 11 13 O2'/Sugar cis y
12 12 38 Watson-Crick/Sugar trans y
13 13 37 Watson-Crick/Hoogsteen trans y
14 16 25 O2'/Sugar ?
15 17 24 Sugar/O2' cis
16 18 33 Watson-Crick/Hoogsteen trans
17 19 23 O2'/Watson-Crick trans y
18 21 22 Watson-Crick/Watson-Crick cis
19 25 36 Watson-Crick/Watson-Crick trans
20 26 27 Watson-Crick/Watson-Crick cis
21 27 36 O2'/Sugar ?
22 28 35 Sugar/O2' ?
23 29 34 Bifurcated/O2' ?
24 30 33 O2'/Bifurcated ?
25 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters