Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb3df41B.m44-434
Source: [PDB-id:chain] 3df4:B (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH HYGROMYCIN B. THIS FILE CONTAINS THE 50S SUBUNIT OF THE SECOND 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.50 ANGSTROMS.
Position (45, 433), (46, 179), (184, 212), (224, 231), (235, 262), (266, 426)
Primary structure ('_': anchors) __-_GAAC_-_AGGAAAAGAAA_-_GAU_-_GCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		12: C2'-endo, 18: C2'-endo, 19: C2'-endo, 23: C2'-endo, 30: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		19: syn, 30: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 4 →
2 3 4 ↑
3 5 6 ↑
4 6 7 ↑
5 9 10 ↑
6 10 11 ↑
7 11 12 ↑
8 13 14 ↑
9 13 38 →
10 14 15 ↑
11 15 16 ↑
12 16 17 ↑
13 17 33 &larr
14 18 24 →
15 18 31 ↑
16 19 21 ↑
17 22 23 ↑
18 24 25 ↑
19 25 26 ↑
20 27 28 ↑
21 28 29 ↑
22 30 34 →
23 32 33 ↑
24 34 35 ↑
25 35 36 ↑
26 38 39 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 12 O2'/Hoogsteen ?
2 1 39 Watson-Crick/Watson-Crick cis
3 2 3 Watson-Crick/Watson-Crick cis
4 6 12 Watson-Crick/Watson-Crick cis
5 6 39 O2'/Sugar ?
6 7 11 Watson-Crick/Watson-Crick cis
7 7 38 Sugar/O2' cis y
8 8 9 Watson-Crick/Watson-Crick cis
9 8 14 Sugar/O2' ?
10 11 13 O2'/Sugar cis y
11 13 37 Watson-Crick/Hoogsteen trans
12 16 25 O2'/Sugar ?
13 16 34 O2'/Bifurcated ?
14 17 24 Sugar/O2' cis y
15 18 31 Hoogsteen/O2' ?
16 18 33 Watson-Crick/Hoogsteen trans
17 19 23 Sugar/Hoogsteen trans
18 21 22 Watson-Crick/Watson-Crick cis
19 24 35 Watson-Crick/Watson-Crick trans
20 25 28 Sugar/Hoogsteen trans y
21 25 36 Watson-Crick/Watson-Crick trans
22 26 27 Watson-Crick/Watson-Crick cis
23 27 36 O2'/Sugar ?
24 28 35 Sugar/O2' ?
25 29 34 Watson-Crick/O2' ?
26 30 33 O2'/Bifurcated ?
27 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters