Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb2qbc1B.m44-434
Source: [PDB-id:chain] 2qbc:B (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH GENTAMICIN. THIS FILE CONTAINS THE 50S SUBUNIT OF THE SECOND 70S RIBOSOME, WITH GENTAMICIN BOUND. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AND IS DESCRIBED IN REMARK 400.
Source: Compound 23S RRNA
Source: Resolution 3.54 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 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 22 23 ↑
17 24 25 ↑
18 25 26 ↑
19 27 28 ↑
20 28 29 ↑
21 30 34 →
22 32 33 ↑
23 34 35 ↑
24 35 36 ↑
25 38 39 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 5 Watson-Crick/Sugar trans y
2 1 12 O2'/Hoogsteen ?
3 1 39 Watson-Crick/Watson-Crick cis
4 2 3 Watson-Crick/Watson-Crick cis
5 6 12 Watson-Crick/Watson-Crick cis
6 6 39 O2'/Sugar ?
7 7 11 Watson-Crick/Watson-Crick cis
8 7 38 Sugar/O2' cis y
9 8 9 Watson-Crick/Watson-Crick cis
10 8 14 Sugar/O2' ?
11 11 13 O2'/Sugar cis y
12 12 38 Watson-Crick/Sugar trans y
13 13 37 Watson-Crick/Hoogsteen trans
14 16 25 O2'/Sugar cis y
15 16 34 O2'/Bifurcated ?
16 17 24 Sugar/O2' cis y
17 17 34 O2'/Watson-Crick ?
18 18 31 Hoogsteen/O2' ?
19 18 33 Watson-Crick/Hoogsteen trans
20 19 23 Sugar/Hoogsteen trans
21 21 22 Watson-Crick/Watson-Crick cis
22 24 35 Watson-Crick/Watson-Crick trans
23 25 28 Sugar/Hoogsteen cis y
24 25 36 Watson-Crick/Watson-Crick trans
25 26 27 Watson-Crick/Watson-Crick cis
26 27 36 O2'/Sugar ?
27 28 35 Sugar/O2' ?
28 30 33 O2'/Bifurcated ?
29 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters