Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-2-5-4-3-0-4-Multiloop pdb2qbk1B.m812-1179
Source: [PDB-id:chain] 2qbk: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 SECOND 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 (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, 15: C4'-exo, 16: C2'-endo, 20: C2'-endo, 21: C2'-endo, 26: C2'-endo, 28: C2'-exo, 33: C2'-exo
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 33 Bifurcated/O2' ?
5 3 34 Watson-Crick/Hoogsteen trans
6 4 14 O2'/Sugar ?
7 4 20 Hoogsteen/Hoogsteen trans
8 5 19 O2'/Bifurcated trans
9 6 7 Watson-Crick/Watson-Crick cis
10 6 14 Bifurcated/Hoogsteen cis y
11 9 13 Watson-Crick/Watson-Crick cis
12 10 11 Watson-Crick/Watson-Crick cis
13 17 18 Watson-Crick/Watson-Crick cis
14 18 21 Bifurcated/O2' ?
15 18 26 Bifurcated/O2' ?
16 20 32 Bifurcated/O2' ?
17 21 26 Bifurcated/O2' ?
18 23 24 Watson-Crick/Watson-Crick cis
19 27 32 O2'/Watson-Crick ?
20 28 29 Watson-Crick/Watson-Crick cis
21 30 31 Watson-Crick/Watson-Crick cis
22 33 34 Hoogsteen/Sugar cis y
23 35 36 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters