Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-7-Internal Loop pdb3cf51X.n1695-1731
Source: [PDB-id:chain] 3cf5:X (&rarr PDB)
Source: Information THIOPEPTIDE ANTIBIOTIC THIOSTREPTON BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS
Source: Compound RRNA-23S RIBOSOMAL RNA
Source: Resolution 3.30 ANGSTROMS.
Position (1701, 1725), (1707, 1717)
Primary structure ('_': anchors) _GCCAA_-_GACGUAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C4'-exo, 3: C4'-exo, 4: C4'-exo, 10: O4'-endo, 15: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 14 ↑
2 2 14 ↓
3 3 5 →
4 5 6 ↑
5 6 7 ↑
6 8 9 ↑
7 9 10 &larr
8 10 12 →
9 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 16 Watson-Crick/Watson-Crick cis
2 2 13 O2'/Bifurcated ?
3 2 14 O2'/Bifurcated ?
4 3 12 Watson-Crick/Watson-Crick trans
5 5 9 Watson-Crick/O2' ?
6 5 10 Bifurcated/O2' ?
7 6 9 O2'/Bifurcated trans
8 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters