Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-5-5-6-Multiloop pdb2d3o10.m43-397
Source: [PDB-id:chain] 2d3o:0 (&rarr PDB)
Source: Information STRUCTURE OF RIBOSOME BINDING DOMAIN OF THE TRIGGER FACTOR ON THE 50S RIBOSOMAL SUBUNIT FROM D. RADIODURANS
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.35 ANGSTROMS.
Position (44, 396), (45, 156), (161, 189), (201, 208), (214, 237), (243, 389)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAAGAAA_-_GAUUC_-_GAUCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-exo, 19: C4'-exo, 24: C2'-exo, 35: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 4 ↑
2 5 6 ↑
3 6 7 ↑
4 9 10 ↑
5 10 11 ↑
6 11 12 ↑
7 13 14 ↑
8 13 42 →
9 14 15 ↑
10 15 16 ↑
11 16 17 ↑
12 17 37 &larr
13 18 24 →
14 18 35 ↑
15 26 27 ↑
16 27 31 →
17 28 30 →
18 29 30 ↑
19 30 31 ↑
20 36 37 ↑
21 38 39 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 12 Hoogsteen/O2' ?
2 1 43 Watson-Crick/Watson-Crick cis
3 2 3 Watson-Crick/Watson-Crick cis
4 4 5 Hoogsteen/O2' ?
5 4 11 Hoogsteen/Watson-Crick trans y
6 6 43 O2'/Sugar ?
7 7 11 Watson-Crick/Watson-Crick cis
8 7 42 Sugar/O2' ?
9 8 9 Watson-Crick/Watson-Crick cis
10 8 14 Sugar/O2' ?
11 11 13 O2'/Sugar cis y
12 16 25 O2'/Sugar ?
13 17 24 Sugar/O2' cis
14 17 38 O2'/Bifurcated ?
15 18 37 Watson-Crick/Hoogsteen trans y
16 19 23 O2'/Bifurcated ?
17 21 22 Watson-Crick/Watson-Crick cis
18 26 31 Watson-Crick/Watson-Crick cis
19 28 29 Watson-Crick/Watson-Crick cis
20 31 40 O2'/Sugar ?
21 32 40 Hoogsteen/O2' ?
22 35 36 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters