Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb3dll1X.n641-673
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 (643, 671), (649, 664)
Primary structure ('_': anchors) _UGAAA_-_CGGAGG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-exo, 13: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		14: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 11 &larr
4 4 5 ↑
5 4 12 →
6 5 6 ↑
7 6 7 ↑
8 8 9 ↑
9 9 10 ↑
10 10 11 ↑
11 12 13 ↑
12 13 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 2 13 Watson-Crick/Watson-Crick cis
3 3 11 Bifurcated/O2' ?
4 3 12 Hoogsteen/Sugar trans y
5 4 10 Bifurcated/O2' ?
6 4 11 O2'/Bifurcated ?
7 5 10 O2'/Bifurcated trans
8 6 9 Watson-Crick/Watson-Crick cis y
9 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters