Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-7-Internal Loop pdb3dll1X.n1707-1717
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 (1701, 1725), (1707, 1717)
Primary structure ('_': anchors) _GCCAA_-_GACGUAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C4'-exo, 10: O4'-endo, 14: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 14 ↓
2 3 5 →
3 5 6 ↑
4 6 7 ↑
5 8 9 ↑
6 9 10 &larr
7 10 12 →
8 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 5 Sugar/O2' ?
2 1 16 Watson-Crick/Watson-Crick cis
3 2 13 O2'/Bifurcated ?
4 2 14 O2'/Bifurcated ?
5 5 10 Bifurcated/O2' ?
6 6 9 Sugar/Hoogsteen trans y
7 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters