Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb2qbi1B.m44-434
Source: [PDB-id:chain] 2qbi:B (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH GENTAMICIN AND RIBOSOME RECYCLING FACTOR (RRF). THIS FILE CONTAINS THE 50S SUBUNIT OF THE FIRST 70S RIBOSOME, WITH GENTAMICIN AND RRF BOUND. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AND IS DESCRIBED IN REMARK 400.
Source: Compound 23S RRNA
Source: Resolution 4.00 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) 		4: C4'-exo, 12: C2'-endo, 18: C3'-exo, 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 1 12 &larr
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 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 13 37 Watson-Crick/Hoogsteen trans
13 16 25 O2'/Sugar ?
14 16 34 O2'/Bifurcated ?
15 17 24 Sugar/O2' cis y
16 17 34 Hoogsteen/Watson-Crick trans y
17 18 31 Hoogsteen/O2' ?
18 18 33 Watson-Crick/Hoogsteen trans
19 19 23 Sugar/Hoogsteen trans
20 21 22 Watson-Crick/Watson-Crick cis
21 24 34 Hoogsteen/Watson-Crick cis y
22 24 35 Watson-Crick/Watson-Crick trans y
23 25 28 Sugar/Hoogsteen trans 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