Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'8-4-0-0-6-11-3-3-6-Multiloop pdb3dll1X.m43-375
Source: [PDB-id:chain] 3dll:X (&rarr PDB)
Source: Information THE OXAZOLIDINONE ANTIBIOTICS PERTURB THE RIBOSOMAL PEPTIDYL-TRANSFERASE CENTER AND EFFECT TRNA POSITIONING
Source: Compound RRNA-23S RIBOSOMAL RNA
Source: Resolution 3.50 ANGSTROMS.
Position (44, 374), (53, 114), (119, 128), (129, 142), (143, 154), (161, 189), (201, 208), (212, 239), (243, 367)
Primary structure ('_': anchors) _CCGAUGAA_-_GAAU_-__-__-_GGGAAC_-_AGGAGAAGAAA_-_GAU_-_UCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		6: C2'-exo, 11: C4'-exo, 13: C2'-exo, 14: C4'-exo, 16: C2'-exo, 18: C2'-exo, 21: C4'-exo, 24: C2'-exo, 34: C2'-exo, 39: C4'-exo, 44: C2'-exo, 54: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 4 22 →
2 5 13 &larr
3 8 9 ↑
4 8 13 →
5 9 10 ↑
6 11 12 ↑
7 12 14 &larr
8 15 20 →
9 16 18 →
10 22 23 ↑
11 23 24 ↑
12 25 26 ↑
13 26 27 ↑
14 29 30 ↑
15 30 31 ↑
16 31 32 ↑
17 33 34 ↑
18 33 58 →
19 34 35 ↑
20 35 36 ↑
21 36 37 ↑
22 37 53 &larr
23 38 44 →
24 38 51 ↑
25 39 41 ↑
26 44 45 ↑
27 47 48 ↑
28 48 49 ↑
29 50 54 →
30 52 53 ↑
31 55 56 ↑
32 58 59 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 59 Watson-Crick/Watson-Crick cis
2 2 23 Watson-Crick/Watson-Crick cis
3 2 31 O2'/Bifurcated ?
4 4 5 Watson-Crick/Sugar cis
5 4 21 O2'/Bifurcated ?
6 7 13 Bifurcated/O2' ?
7 7 14 Bifurcated/O2' ?
8 7 15 Watson-Crick/Watson-Crick trans y
9 8 12 Watson-Crick/O2' ?
10 8 14 Bifurcated/O2' trans y
11 8 22 O2'/Watson-Crick trans
12 9 12 O2'/Bifurcated trans
13 10 11 Watson-Crick/Watson-Crick cis
14 16 17 Watson-Crick/Watson-Crick cis
15 18 19 Watson-Crick/Watson-Crick cis
16 20 21 Watson-Crick/Watson-Crick cis
17 24 25 Hoogsteen/O2' ?
18 24 31 Hoogsteen/Watson-Crick trans y
19 26 32 Watson-Crick/Watson-Crick cis y
20 26 59 O2'/Sugar cis y
21 27 31 Watson-Crick/Watson-Crick cis
22 27 58 Sugar/O2' ?
23 28 29 Watson-Crick/Watson-Crick cis
24 31 33 O2'/Sugar cis y
25 33 57 Watson-Crick/Hoogsteen trans y
26 36 45 O2'/Sugar ?
27 36 54 O2'/Bifurcated ?
28 37 44 Sugar/O2' ?
29 37 54 O2'/Bifurcated ?
30 38 53 Watson-Crick/Hoogsteen trans y
31 39 41 C/O2' ?
32 39 43 O2'/Watson-Crick trans y
33 41 42 Watson-Crick/Watson-Crick cis
34 46 47 Watson-Crick/Watson-Crick cis
35 47 56 O2'/Sugar ?
36 48 55 Sugar/O2' ?
37 49 54 Bifurcated/O2' ?
38 50 53 O2'/Bifurcated ?
39 51 52 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters