Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb1j5a1A.m43-402
Source: [PDB-id:chain] 1j5a:A (&rarr PDB)
Source: Information STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA
Source: Compound 23S RRNA
Source: Resolution 3.50 ANGSTROMS.
Position (44, 401), (45, 156), (161, 189), (201, 208), (212, 239), (243, 394)
Primary structure ('_': anchors) __-_GAAC_-_AGGAGAAGAAA_-_GAU_-_UCA_-_UAAAUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-exo, 30: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		30: 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 13 14 ↑
8 13 38 →
9 14 15 ↑
10 15 16 ↑
11 16 17 ↑
12 17 33 &larr
13 18 24 →
14 18 31 ↑
15 19 21 ↑
16 22 23 ↑
17 24 25 ↑
18 25 26 ↑
19 27 28 ↑
20 28 29 ↑
21 30 34 →
22 32 33 ↑
23 34 35 ↑
24 35 36 ↑
25 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 4 5 Hoogsteen/O2' ?
4 4 12 Hoogsteen/Watson-Crick trans y
5 7 11 Watson-Crick/Watson-Crick cis
6 7 38 Sugar/O2' ?
7 8 9 Watson-Crick/Watson-Crick cis
8 11 13 O2'/Sugar ?
9 13 37 Watson-Crick/Hoogsteen trans
10 16 25 O2'/Sugar ?
11 17 24 Sugar/O2' cis y
12 17 34 O2'/Watson-Crick ?
13 18 30 O2'/Watson-Crick ?
14 18 33 Watson-Crick/Hoogsteen trans y
15 19 23 O2'/Watson-Crick trans y
16 21 22 Watson-Crick/Watson-Crick cis
17 24 35 Watson-Crick/Watson-Crick trans y
18 25 36 Watson-Crick/Watson-Crick trans y
19 26 27 Watson-Crick/Watson-Crick cis
20 27 36 O2'/Sugar ?
21 28 35 Sugar/O2' ?
22 30 33 O2'/Bifurcated ?
23 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters