Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'0-4-11-3-3-6-Multiloop pdb1k011A.m43-402
Source: [PDB-id:chain] 1k01: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 31 ↑
14 19 21 ↑
15 22 23 ↑
16 24 25 ↑
17 25 26 ↑
18 27 28 ↑
19 28 29 ↑
20 30 34 →
21 32 33 ↑
22 34 35 ↑
23 35 36 ↑
24 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 6 12 Watson-Crick/Watson-Crick cis y
6 7 11 Watson-Crick/Watson-Crick cis
7 7 38 Sugar/O2' ?
8 8 9 Watson-Crick/Watson-Crick cis
9 11 13 O2'/Sugar ?
10 13 37 Watson-Crick/Hoogsteen trans
11 16 25 O2'/Sugar ?
12 17 24 Sugar/O2' cis y
13 17 34 O2'/Watson-Crick ?
14 18 30 O2'/Watson-Crick ?
15 18 33 Watson-Crick/Hoogsteen trans y
16 19 23 O2'/Watson-Crick trans y
17 21 22 Watson-Crick/Watson-Crick cis
18 24 35 Watson-Crick/Watson-Crick trans y
19 25 36 Watson-Crick/Watson-Crick trans y
20 26 27 Watson-Crick/Watson-Crick cis
21 27 36 O2'/Sugar ?
22 28 35 Sugar/O2' ?
23 30 33 O2'/Bifurcated ?
24 31 32 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters