Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'13-6-12-4-9-13-4-4-9-Multiloop pdb2gya10.m22-385
Source: [PDB-id:chain] 2gya:0 (&rarr PDB)
Source: Information STRUCTURE OF THE 50S SUBUNIT OF A PRE-TRANSLOCATIONAL E. COLI RIBOSOME OBTAINED BY FITTING ATOMIC MODELS FOR RNA AND PROTEIN COMPONENTS INTO CRYO-EM MAP EMD-1056
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.00 ANGSTROMS.
Position (27, 380), (41, 54), (61, 92), (105, 111), (116, 130), (140, 164), (178, 185), (190, 215), (220, 370)
Primary structure ('_': anchors) _AGGCGAUGAAGGA_-_AUAAGC_-_GAUUUCCGAAUG_-_CCGA_-_GGCGAACCG_-_CGAGGAAAAGAAA_-_GAUU_-_AGCA_-_UAAAUACUC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		7: C2'-exo, 35: C4'-exo, 38: C2'-exo, 39: C2'-exo, 40: C2'-exo, 45: C4'-exo, 46: C2'-exo, 66: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		7: syn, 20: syn, 33: syn, 40: syn, 45: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 4 5 ↑
4 5 6 ↑
5 6 46 →
6 10 11 ↑
7 11 12 ↑
8 12 13 ↑
9 13 14 ↑
10 14 15 ↑
11 17 19 →
12 25 26 ↑
13 26 27 ↑
14 27 28 ↑
15 29 30 ↑
16 30 31 ↑
17 31 32 ↑
18 32 34 &larr
19 33 34 →
20 35 42 →
21 36 37 ↑
22 36 40 ↓
23 42 43 ↑
24 44 45 &larr
25 46 47 ↑
26 47 48 ↑
27 49 50 ↑
28 50 51 ↑
29 52 53 ↑
30 53 54 ↑
31 53 57 →
32 56 57 ↑
33 58 59 ↑
34 59 60 ↑
35 61 62 ↑
36 62 63 ↑
37 64 65 ↑
38 65 83 &larr
39 66 72 →
40 66 81 ↑
41 67 69 ↑
42 70 71 ↑
43 72 73 ↑
44 73 74 ↑
45 74 75 ↑
46 76 77 ↑
47 77 78 ↑
48 78 79 ↑
49 82 83 ↑
50 84 85 ↑
51 85 86 ↑
52 89 90 ↑
53 91 92 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 90 Watson-Crick/Watson-Crick trans y
2 1 92 Watson-Crick/Watson-Crick cis
3 3 89 Watson-Crick/Watson-Crick cis
4 7 9 Sugar/O2' ?
5 7 44 O2'/Bifurcated ?
6 9 32 Watson-Crick/O2' ?
7 9 33 Bifurcated/O2' ?
8 9 34 Bifurcated/O2' ?
9 14 16 Watson-Crick/Hoogsteen cis y
10 15 16 Watson-Crick/Watson-Crick cis
11 16 19 Sugar/O2' ?
12 16 21 Watson-Crick/O2' ?
13 23 24 Watson-Crick/Watson-Crick cis y
14 36 39 O2'/Bifurcated ?
15 37 38 Watson-Crick/Watson-Crick cis y
16 37 39 Watson-Crick/Watson-Crick cis y
17 43 44 Watson-Crick/Watson-Crick cis y
18 50 60 Watson-Crick/Watson-Crick cis y
19 51 59 Watson-Crick/Watson-Crick cis
20 52 57 Watson-Crick/Watson-Crick cis y
21 52 62 Sugar/O2' ?
22 54 55 Watson-Crick/Watson-Crick cis
23 59 61 O2'/Sugar ?
24 64 73 O2'/Sugar ?
25 64 84 O2'/Bifurcated ?
26 65 72 Sugar/O2' cis y
27 65 84 O2'/Watson-Crick ?
28 66 80 O2'/Watson-Crick ?
29 66 83 Watson-Crick/Hoogsteen trans
30 67 71 O2'/Bifurcated trans y
31 69 70 Watson-Crick/Watson-Crick cis
32 72 85 Watson-Crick/Watson-Crick trans y
33 73 86 Watson-Crick/Watson-Crick trans y
34 75 76 Watson-Crick/Watson-Crick cis
35 78 85 Sugar/O2' ?
36 79 84 Watson-Crick/O2' ?
37 80 83 O2'/Watson-Crick ?
38 81 82 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters