Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-2-5-4-3-0-4-Multiloop pdb2qbc1B.m812-1179
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 (817, 1174), (822, 835), (838, 924), (930, 955), (960, 971), (975, 1147), (1148, 1169)
Primary structure ('_': anchors) _GAAA_-_GC_-_AGACA_-_AAGA_-_AGA_-__-_GGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 16: C2'-endo, 20: C2'-endo, 21: C2'-endo, 26: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		21: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 33 &larr
3 3 4 ↑
4 3 35 →
5 4 5 ↑
6 5 17 ↑
7 6 8 →
8 7 8 ↑
9 8 9 ↑
10 11 12 ↑
11 12 13 ↑
12 13 14 ↑
13 14 15 ↑
14 18 19 ↑
15 19 20 &larr
16 20 34 →
17 21 26 ↓
18 21 32 ↑
19 22 23 ↑
20 22 27 →
21 24 25 ↑
22 28 31 ↓
23 29 30 ↑
24 32 33 ↑
25 35 36 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 36 Watson-Crick/Watson-Crick cis
2 2 34 O2'/Watson-Crick ?
3 2 35 Bifurcated/O2' trans
4 3 13 Sugar/Sugar trans y
5 3 33 Bifurcated/O2' ?
6 3 34 Watson-Crick/Hoogsteen trans
7 4 14 O2'/Sugar ?
8 4 20 Hoogsteen/Hoogsteen trans
9 5 19 Sugar/Hoogsteen trans
10 6 7 Watson-Crick/Watson-Crick cis
11 6 14 Bifurcated/Hoogsteen cis y
12 9 13 Watson-Crick/Watson-Crick cis
13 10 11 Watson-Crick/Watson-Crick cis
14 17 18 Watson-Crick/Watson-Crick cis
15 18 21 Bifurcated/O2' ?
16 18 26 Watson-Crick/O2' ?
17 20 32 Bifurcated/O2' ?
18 21 26 Bifurcated/O2' ?
19 22 26 Sugar/Hoogsteen trans y
20 23 24 Watson-Crick/Watson-Crick cis
21 28 29 Watson-Crick/Watson-Crick cis
22 30 31 Watson-Crick/Watson-Crick cis
23 33 34 Hoogsteen/Sugar cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters