Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-43-0-43-6-2-Multiloop pdb2b661A.m255-453
Source: [PDB-id:chain] 2b66:A (&rarr PDB)
Source: Information 50S RIBOSOMAL SUBUNIT FROM A CRYSTAL STRUCTURE OF RELEASE FACTOR RF1, TRNAS AND MRNA BOUND TO THE RIBOSOME. THIS FILE CONTAINS THE 50S SUBUNIT FROM A CRYSTAL STRUCTURE OF RELEASE FACTOR RF1, TRNAS AND MRNA BOUND TO THE RIBOSOME AND IS DESCRIBED IN REMARK 400
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 5.90 ANGSTROMS.
Position (257, 451), (263, 281), (325, 340), (341, 358), (402, 426), (433, 448)
Primary structure ('_': anchors) _UAAAC_-_GGGUCGUGGGGCCCUCGGACACCGAAUCCCCAGCCUAGCCGAA_-__-_CCCGUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUA_-_GAAUCU_-_AA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 5: O4'-exo, 10: C4'-exo, 11: C4'-exo, 14: C1'-exo, 15: C2'-endo, 18: C2'-exo, 20: C2'-exo, 26: C2'-exo, 27: C2'-exo, 28: C4'-exo, 30: C2'-exo, 31: C2'-exo, 32: C1'-endo, 33: C2'-exo, 35: C4'-exo, 37: C2'-exo, 40: O4'-endo, 41: C2'-exo, 44: C2'-exo, 46: C2'-exo, 49: C2'-exo, 50: C2'-exo, 52: C4'-exo, 53: C2'-exo, 58: C4'-exo, 59: O4'-endo, 60: C2'-exo, 61: C2'-exo, 63: C4'-exo, 68: C2'-exo, 69: C2'-exo, 73: C2'-exo, 79: C2'-exo, 81: C4'-exo, 88: C4'-exo, 90: C2'-exo, 94: C2'-exo, 95: O4'-endo, 96: C2'-exo, 98: C4'-exo, 100: C2'-exo, 102: C2'-exo, 104: C2'-endo, 105: C1'-endo, 108: C4'-exo, 109: C4'-exo, 110: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		4: syn, 14: syn, 25: syn, 44: syn, 81: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 8 9 ↑
3 17 18 ↑
4 17 93 →
5 18 19 ↑
6 19 20 ↑
7 23 86 →
8 24 25 &larr
9 36 37 ↑
10 41 42 ↑
11 42 43 ↑
12 47 48 ↑
13 48 49 ↑
14 50 51 ↑
15 52 54 →
16 60 61 ↑
17 62 63 ↑
18 63 64 ↑
19 69 70 ↑
20 72 73 ↑
21 73 74 ↑
22 74 75 ↑
23 77 78 ↑
24 86 87 ↑
25 87 88 ↑
26 88 89 ↑
27 98 99 ↑
28 98 102 →
29 102 103 ↑
30 109 110 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 111 Watson-Crick/Watson-Crick cis y
2 3 10 Watson-Crick/O2' ?
3 3 11 Bifurcated/O2' ?
4 5 6 Bifurcated/O2' ?
5 7 8 Watson-Crick/Watson-Crick cis
6 12 14 O2'/Watson-Crick ?
7 16 93 Watson-Crick/Watson-Crick cis
8 18 91 Watson-Crick/Watson-Crick cis y
9 21 87 Watson-Crick/Watson-Crick cis
10 23 85 Watson-Crick/Watson-Crick cis y
11 30 80 Sugar/O2' ?
12 31 32 C/O2' ?
13 31 34 Watson-Crick/Watson-Crick cis y
14 31 81 Watson-Crick/Sugar cis y
15 33 81 Watson-Crick/Hoogsteen trans y
16 35 77 Watson-Crick/Watson-Crick cis
17 36 76 Hoogsteen/Watson-Crick cis y
18 37 76 Watson-Crick/Watson-Crick cis
19 38 73 Hoogsteen/Watson-Crick trans y
20 38 74 Watson-Crick/Watson-Crick cis y
21 39 40 O2'/Bifurcated ?
22 40 72 Hoogsteen/O2' ?
23 41 71 O2'/Bifurcated ?
24 43 69 Watson-Crick/Watson-Crick cis
25 46 59 Bifurcated/O2' ?
26 47 59 Watson-Crick/O2' trans y
27 47 63 Watson-Crick/Watson-Crick cis y
28 47 65 Bifurcated/Watson-Crick cis
29 48 63 Watson-Crick/Watson-Crick cis
30 49 62 Bifurcated/O2' ?
31 52 53 Watson-Crick/Watson-Crick cis
32 54 55 Watson-Crick/Watson-Crick cis
33 55 56 Bifurcated/O2' ?
34 67 68 Hoogsteen/O2' ?
35 75 76 Hoogsteen/Sugar cis y
36 79 80 Hoogsteen/O2' ?
37 80 81 C/O2' ?
38 89 90 Hoogsteen/O2' ?
39 94 110 O2'/Bifurcated ?
40 95 110 Hoogsteen/O2' ?
41 95 111 O2'/Hoogsteen ?
42 97 99 Bifurcated/O2' ?
43 99 100 Watson-Crick/Watson-Crick cis y
44 102 110 Watson-Crick/Watson-Crick trans y
45 103 107 O2'/Sugar ?
46 103 110 Watson-Crick/Watson-Crick trans y
47 107 108 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters