Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'8-5-Internal Loop pdb3dllFX.n619-740
Source: [PDB-id:chain] 3dll:X (&rarr PDB)
Source: Information THE OXAZOLIDINONE ANTIBIOTICS PERTURB THE RIBOSOMAL PEPTIDYL-TRANSFERASE CENTER AND EFFECT TRNA POSITIONING
Source: Compound RRNA-23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.50 ANGSTROMS.
Position (613, 749), (619, 740)
Primary structure ('_': anchors) _AGAUAGCU_-_CGAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C4'-exo, 5: C4'-exo, 7: C2'-exo, 8: C4'-exo, 13: C4'-exo, 14: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		13: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 5 6 ↑
3 5 14 →
4 5 15 &larr
5 6 7 ↑
6 7 12 →
7 9 10 &larr
8 11 12 ↑
9 13 14 &larr
10 15 16 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 17 Watson-Crick/Watson-Crick cis
2 2 16 Watson-Crick/Watson-Crick cis y
3 3 4 Bifurcated/O2' ?
4 3 15 Watson-Crick/Watson-Crick cis
5 6 14 Watson-Crick/Hoogsteen trans
6 8 16 Bifurcated/O2' ?
7 8 17 Bifurcated/O2' ?
8 10 11 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters