Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-3-Internal Loop pdb1kd11A.n1274-1318
Source: [PDB-id:chain] 1kd1:A (&rarr PDB)
Source: Information CO-CRYSTAL STRUCTURE OF SPIRAMYCIN BOUND TO THE 50S RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RRNA
Source: Resolution 3.00 ANGSTROMS.
Position (1281, 1311), (1288, 1307)
Primary structure ('_': anchors) _AUGGAA_-_GGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 4: C2'-endo, 5: C2'-endo, 6: C2'-exo, 11: C2'-endo, 12: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 13 →
3 3 12 ↓
4 5 11 &larr
5 6 7 ↑
6 6 12 →
7 7 8 ↑
8 9 10 ↑
9 10 11 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 12 Watson-Crick/O2' ?
3 5 11 O2'/Bifurcated ?
4 5 12 Hoogsteen/Sugar trans
5 6 10 Bifurcated/O2' ?
6 6 11 Sugar/Hoogsteen trans y
7 6 13 O2'/Sugar ?
8 7 10 O2'/Bifurcated trans
9 8 9 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters