Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-43-0-43-6-2-Multiloop pdb2b9p1A.m255-453
Source: [PDB-id:chain] 2b9p:A (&rarr PDB)
Source: Information 50S RIBOSOMAL SUBUNIT FROM A CRYSTAL STRUCTURE OF THE RIBOSOME IN COMPLEX WITH TRNAS AND MRNA WITH A STOP CODON IN THE A-SITE. THIS FILE CONTAINS THE 50S SUBUNIT FROM A CRYSTAL STRUCTURE OF THE RIBOSOME IN COMPLEX WITH TRNAS AND MRNA WITH A STOP CODON IN THE A-SITE AND IS DESCRIBED IN REMARK 400.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 6.46 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, 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 50 51 ↑
14 52 54 →
15 60 61 ↑
16 62 63 ↑
17 63 64 ↑
18 69 70 ↑
19 72 73 ↑
20 73 74 ↑
21 74 75 ↑
22 77 78 ↑
23 86 87 ↑
24 87 88 ↑
25 88 89 ↑
26 98 99 ↑
27 98 102 →
28 102 103 ↑
29 109 110 ↑
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 4 93 O2'/Sugar ?
5 5 6 Bifurcated/O2' ?
6 7 8 Watson-Crick/Watson-Crick cis
7 12 14 O2'/Watson-Crick ?
8 16 93 Watson-Crick/Watson-Crick cis
9 18 91 Watson-Crick/Watson-Crick cis y
10 21 87 Watson-Crick/Watson-Crick cis
11 23 85 Watson-Crick/Watson-Crick cis y
12 30 80 Sugar/O2' ?
13 31 32 Sugar/O2' ?
14 31 34 Watson-Crick/Watson-Crick cis y
15 31 81 Watson-Crick/Sugar cis y
16 33 81 Watson-Crick/Hoogsteen trans y
17 35 77 Watson-Crick/Watson-Crick cis
18 36 76 Hoogsteen/Watson-Crick cis y
19 37 76 Watson-Crick/Watson-Crick cis
20 38 73 Hoogsteen/Watson-Crick trans y
21 38 74 Watson-Crick/Watson-Crick cis y
22 39 40 O2'/Bifurcated ?
23 40 72 Hoogsteen/O2' ?
24 41 71 O2'/Bifurcated ?
25 43 69 Watson-Crick/Watson-Crick cis
26 46 59 Bifurcated/O2' ?
27 47 59 Bifurcated/O2' ?
28 47 63 Watson-Crick/Watson-Crick cis y
29 47 65 Bifurcated/Watson-Crick cis
30 48 63 Watson-Crick/Watson-Crick cis
31 49 62 Watson-Crick/O2' ?
32 52 53 Watson-Crick/Watson-Crick cis
33 54 55 Watson-Crick/Watson-Crick cis
34 55 56 Bifurcated/O2' ?
35 67 68 Hoogsteen/O2' ?
36 75 76 C/O2' cis y
37 79 80 Hoogsteen/O2' ?
38 80 81 C/O2' ?
39 89 90 Hoogsteen/O2' ?
40 94 110 O2'/Bifurcated ?
41 95 110 Hoogsteen/O2' ?
42 95 111 O2'/Hoogsteen ?
43 97 99 Bifurcated/O2' ?
44 99 100 Watson-Crick/Watson-Crick cis y
45 102 110 Watson-Crick/Watson-Crick trans y
46 103 107 O2'/Sugar ?
47 103 110 Watson-Crick/Watson-Crick trans y
48 107 108 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters