Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'2-4-11-3-3-9-Multiloop pdb1vq910.m25-440
Source: [PDB-id:chain] 1vq9:0 (&rarr PDB)
Source: Information THE STRUCTURE OF CCA-PHE-CAP-BIO AND THE ANTIBIOTIC SPARSOMYCIN BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.40 ANGSTROMS.
Position (30, 435), (33, 141), (146, 174), (186, 194), (198, 225), (229, 425)
Primary structure ('_': anchors) _CG_-_GAAC_-_AGGAACAGAAA_-_GAU_-_ACA_-_UAAACACAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		14: C2'-endo, 16: C2'-exo, 20: C3'-exo, 21: C2'-endo, 25: C2'-endo, 32: C2'-endo, 39: C2'-endo, 42: C2'-endo
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 3 ↑
3 5 6 ↑
4 7 8 ↑
5 7 43 →
6 8 9 ↑
7 11 12 ↑
8 12 13 ↑
9 13 14 ↑
10 15 16 ↑
11 15 40 →
12 16 17 ↑
13 17 18 ↑
14 18 19 ↑
15 19 35 &larr
16 20 26 →
17 20 33 ↑
18 21 23 ↑
19 24 25 ↑
20 26 27 ↑
21 27 28 ↑
22 28 38 ↓
23 29 30 ↑
24 30 31 ↑
25 32 36 ↑
26 34 35 ↑
27 36 37 ↑
28 37 38 ↑
29 40 41 ↑
30 41 42 ↑
31 43 44 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 44 Watson-Crick/Watson-Crick cis
2 2 42 Watson-Crick/Watson-Crick cis
3 2 43 Watson-Crick/Watson-Crick cis y
4 3 41 Watson-Crick/Watson-Crick cis
5 4 5 Watson-Crick/Watson-Crick cis
6 4 13 O2'/Bifurcated ?
7 6 7 Hoogsteen/O2' ?
8 8 14 Watson-Crick/Watson-Crick cis
9 8 41 O2'/Sugar cis y
10 9 13 Watson-Crick/Watson-Crick cis
11 9 40 Sugar/O2' cis y
12 10 11 Watson-Crick/Watson-Crick cis
13 10 16 Sugar/O2' ?
14 13 15 O2'/Sugar cis y
15 14 40 Watson-Crick/Sugar trans y
16 18 27 O2'/Sugar ?
17 19 26 Sugar/O2' cis y
18 19 36 O2'/Watson-Crick trans y
19 20 32 O2'/Watson-Crick ?
20 20 33 Hoogsteen/O2' ?
21 20 35 Watson-Crick/Hoogsteen trans
22 21 25 Sugar/Hoogsteen trans
23 23 24 Watson-Crick/Watson-Crick cis
24 26 37 Watson-Crick/Watson-Crick trans
25 27 38 Watson-Crick/Watson-Crick trans
26 28 29 Watson-Crick/Watson-Crick cis
27 28 39 Bifurcated/O2' ?
28 30 37 Sugar/O2' ?
29 31 36 Watson-Crick/O2' ?
30 32 35 O2'/Watson-Crick trans y
31 32 36 Bifurcated/O2' ?
32 33 34 Watson-Crick/Watson-Crick cis
33 42 43 Hoogsteen/Sugar cis y
34 42 44 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters