Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-2-5-4-3-0-4-Multiloop pdb1qvf10.m899-1269
Source: [PDB-id:chain] 1qvf:0 (&rarr PDB)
Source: Information STRUCTURE OF A DEACYLATED TRNA MINIHELIX BOUND TO THE E SITE OF THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.10 ANGSTROMS.
Position (904, 1264), (909, 922), (925, 1008), (1014, 1038), (1043, 1054), (1058, 1236), (1237, 1259)
Primary structure ('_': anchors) _GAAA_-_AC_-_AUUCC_-_AGGA_-_AGA_-__-_AGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		16: C1'-exo, 20: C2'-endo, 21: C1'-exo, 26: C2'-endo, 27: C2'-endo, 31: C1'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		26: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 33 &larr
3 3 4 ↑
4 3 35 →
5 4 5 ↑
6 5 17 ↑
7 7 8 ↑
8 8 9 ↑
9 11 12 ↑
10 12 13 ↑
11 13 14 ↑
12 18 19 ↑
13 19 20 &larr
14 20 34 →
15 21 26 &larr
16 21 32 →
17 22 23 ↑
18 22 27 →
19 24 25 ↑
20 28 30 →
21 28 31 ↓
22 32 33 ↑
23 35 36 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 36 Watson-Crick/Watson-Crick cis
2 2 34 O2'/Bifurcated ?
3 2 35 Bifurcated/O2' trans
4 3 33 Bifurcated/O2' ?
5 3 34 Watson-Crick/Hoogsteen trans
6 4 14 O2'/Sugar ?
7 4 20 Hoogsteen/Hoogsteen trans y
8 5 19 Sugar/Hoogsteen trans
9 6 7 Watson-Crick/Watson-Crick cis
10 8 13 Watson-Crick/Watson-Crick cis y
11 9 12 Bifurcated/Watson-Crick trans
12 10 11 Watson-Crick/Watson-Crick cis
13 12 36 O2'/Sugar ?
14 13 35 Sugar/O2' ?
15 17 18 Watson-Crick/Watson-Crick cis
16 18 21 Hoogsteen/O2' ?
17 18 26 Watson-Crick/O2' ?
18 21 26 O2'/Bifurcated ?
19 21 27 Hoogsteen/Sugar trans
20 22 26 Sugar/Hoogsteen trans y
21 23 24 Watson-Crick/Watson-Crick cis
22 27 32 O2'/Watson-Crick ?
23 28 29 Watson-Crick/Watson-Crick cis
24 30 31 Watson-Crick/Watson-Crick cis
25 33 34 Hoogsteen/Sugar cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters