Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-9-Internal Loop pdb3dll1X.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
Source: Resolution 3.50 ANGSTROMS.
Position (1350, 1502), (1355, 1492)
Primary structure ('_': anchors) _GGAC_-_CAAGAAAAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 3: C2'-exo, 5: C2'-exo, 8: C4'-exo, 9: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 6 11 ↓
4 8 10 ↑
5 12 13 ↑
6 13 14 ↑
7 14 15 ↑
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 13 O2'/Sugar ?
4 4 14 O2'/Bifurcated ?
5 6 7 Watson-Crick/Watson-Crick cis
6 8 11 Watson-Crick/Watson-Crick cis
7 10 11 Sugar/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters