Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-3-1-2-14-18-Multiloop pdb1j5a1A.m1996-2338
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 (1998, 2336), (2002, 2143), (2147, 2157), (2159, 2181), (2184, 2284), (2299, 2317)
Primary structure ('_': anchors) _UUU_-_UUG_-_C_-_GC_-_CUUAGUGAACCGGU_-_AUCGAUCAACGGAUAAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		None
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		26: syn, 47: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 5 52 →
3 7 8 ↑
4 9 10 ↑
5 9 43 →
6 13 44 ↓
7 14 15 ↑
8 15 42 ↑
9 16 17 ↑
10 16 23 ↓
11 19 20 ↑
12 20 21 ↑
13 26 27 →
14 26 46 &larr
15 27 28 ↑
16 28 29 ↑
17 29 30 ↑
18 30 38 →
19 31 32 ↑
20 31 37 →
21 32 33 ↑
22 34 35 ↑
23 35 36 ↑
24 36 37 ↑
25 39 41 ↑
26 52 53 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 53 Watson-Crick/Watson-Crick cis
2 3 5 Hoogsteen/Watson-Crick cis
3 5 6 Watson-Crick/Watson-Crick cis
4 5 51 O2'/Sugar ?
5 6 51 Watson-Crick/O2' ?
6 7 52 Hoogsteen/Watson-Crick cis
7 8 53 Hoogsteen/Watson-Crick cis y
8 10 11 Watson-Crick/Watson-Crick cis y
9 12 43 O2'/Bifurcated ?
10 13 14 Watson-Crick/Watson-Crick cis
11 15 44 Watson-Crick/Watson-Crick cis y
12 17 18 Watson-Crick/Watson-Crick cis
13 25 26 Sugar/O2' ?
14 26 39 Bifurcated/O2' ?
15 27 39 Watson-Crick/Hoogsteen trans y
16 29 38 Watson-Crick/Watson-Crick cis
17 31 36 Watson-Crick/Watson-Crick cis
18 32 35 Bifurcated/Watson-Crick cis y
19 33 34 Watson-Crick/Watson-Crick cis y
20 48 49 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters