Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb2qp11B.m44-434
Source: [PDB-id:chain] 2qp1:B (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH SPECTINOMYCIN AND NEOMYCIN. THIS FILE CONTAINS THE 50S SUBUNIT OF THE SECOND 70S RIBOSOME, WITH NEOMYCIN BOUND. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES.
Source: Compound 23S RRNA
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
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' ?
8 8 9 Watson-Crick/Watson-Crick cis
9 8 14 Sugar/O2' ?
10 11 13 O2'/Sugar cis y
11 12 38 Watson-Crick/Sugar trans y
12 13 37 Watson-Crick/Hoogsteen trans
13 16 25 O2'/Sugar cis y
14 17 24 Sugar/O2' cis y
15 18 30 Hoogsteen/Watson-Crick cis y
16 18 31 Hoogsteen/O2' ?
17 18 33 Watson-Crick/Hoogsteen trans
18 19 23 Sugar/Hoogsteen trans
19 21 22 Watson-Crick/Watson-Crick cis
20 24 35 Watson-Crick/Watson-Crick trans
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