Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-4-Internal Loop pdb3dllFX.n1349-1503
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 (1350, 1502), (1355, 1492)
Primary structure ('_': anchors) _CAAGAAAAG_-_GGAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		9: C4'-exo, 10: C4'-exo, 13: C2'-exo, 15: C2'-exo, 16: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		7: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 4 5 ↑
5 5 6 ↑
6 7 12 ↓
7 8 10 ↑
8 15 16 ↑
9 16 17 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 17 Watson-Crick/Watson-Crick cis
2 3 15 Hoogsteen/Sugar trans
3 4 14 O2'/Bifurcated ?
4 5 14 O2'/Sugar ?
5 7 8 Sugar/O2' ?
6 7 10 Watson-Crick/Watson-Crick cis
7 11 12 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters