Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb3df11A.n412-423
Source: [PDB-id:chain] 3df1: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 FIRST 70S RIBOSOME, WITH HYGROMYCIN B BOUND. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES.
Source: Compound 16S RIBOSOMAL RNA
Source: Resolution 3.50 ANGSTROMS.
Position (405, 429), (412, 423)
Primary structure ('_': anchors) _GAAGAA_-_GUAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 4: C2'-endo, 5: C4'-exo, 10: C2'-endo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		4: syn, 7: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 11 &larr
3 3 11 →
4 6 7 &larr
5 6 13 →
6 7 8 →
7 9 10 &larr
8 10 12 →
9 12 13 ↑
10 13 14 ↑
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 11 O2'/Hoogsteen ?
3 2 14 Hoogsteen/Sugar trans
4 3 4 Sugar/O2' ?
5 3 5 O2'/Sugar ?
6 3 12 Hoogsteen/Watson-Crick trans
7 5 10 Bifurcated/O2' ?
8 6 10 Bifurcated/O2' ?
9 6 12 Watson-Crick/Hoogsteen trans y
10 8 9 Watson-Crick/Watson-Crick cis
11 11 13 Hoogsteen/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters