Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb3df3FA.n412-423
Source: [PDB-id:chain] 3df3:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROM ESCHERICHIA COLI IN COMPLEX WITH HYGROMYCIN B. THIS FILE CONTAINS THE 30S SUBUNIT OF THE SECOND 70S RIBOSOME, WITH HYGROMYCIN B BOUND. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES.
Source: Compound 16S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.50 ANGSTROMS.
Position (405, 429), (412, 423)
Primary structure ('_': anchors) _GUAAA_-_GAAGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-endo, 6: C2'-endo, 11: C4'-exo, 12: C2'-endo, 13: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 9: syn, 12: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 3 10 →
5 4 6 →
6 5 13 →
7 5 14 &larr
8 6 7 &larr
9 8 9 →
10 9 10 &larr
11 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 2 14 Hoogsteen/Sugar trans
3 3 5 Hoogsteen/Watson-Crick cis
4 4 10 Watson-Crick/Hoogsteen trans y
5 4 13 Hoogsteen/Watson-Crick trans
6 5 14 O2'/Hoogsteen ?
7 6 10 Bifurcated/O2' ?
8 6 11 Bifurcated/O2' ?
9 7 8 Watson-Crick/Watson-Crick cis
10 11 13 O2'/Watson-Crick ?
11 12 13 Sugar/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters