Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb2aar10.m43-397
Source: [PDB-id:chain] 2aar:0 (&rarr PDB)
Source: Information STRUCTURE OF TRIGGER FACTOR BINDING DOMAIN IN BIOLOGICALLY HOMOLOGOUS COMPLEX WITH EUBACTERIAL RIBOSOME.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.50 ANGSTROMS.
Position (44, 396), (45, 156), (161, 189), (201, 208), (212, 239), (243, 389)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAAGAAA_-_GAU_-_UCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-exo, 18: C4'-exo, 19: C4'-exo, 24: C2'-exo, 34: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		19: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 12 &larr
2 3 4 ↑
3 5 6 ↑
4 6 7 ↑
5 9 10 ↑
6 10 11 ↑
7 11 12 ↑
8 13 14 ↑
9 13 38 →
10 14 15 ↑
11 15 16 ↑
12 16 17 ↑
13 17 33 &larr
14 18 24 →
15 18 31 ↑
16 27 28 ↑
17 32 33 ↑
18 35 36 ↑
19 38 39 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 39 Watson-Crick/Watson-Crick cis
2 2 3 Watson-Crick/Watson-Crick cis
3 2 11 O2'/Bifurcated ?
4 4 5 Hoogsteen/O2' ?
5 4 11 Hoogsteen/Watson-Crick trans y
6 5 12 Watson-Crick/Bifurcated cis y
7 6 12 Watson-Crick/Watson-Crick cis y
8 6 39 O2'/Sugar ?
9 7 11 Watson-Crick/Watson-Crick cis
10 7 38 Sugar/O2' cis y
11 8 9 Watson-Crick/Watson-Crick cis
12 11 13 O2'/Sugar cis y
13 13 37 Watson-Crick/Hoogsteen trans
14 16 25 O2'/Sugar ?
15 16 34 O2'/Bifurcated ?
16 17 24 Sugar/O2' cis
17 17 34 O2'/Bifurcated ?
18 18 33 Watson-Crick/Hoogsteen trans
19 19 23 O2'/Watson-Crick ?
20 21 22 Watson-Crick/Watson-Crick cis
21 25 36 Watson-Crick/Watson-Crick trans y
22 26 27 Watson-Crick/Watson-Crick cis y
23 27 36 O2'/Sugar cis y
24 28 35 Sugar/O2' ?
25 30 33 O2'/Watson-Crick ?
26 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters