Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb3d5c1A.n407-418
Source: [PDB-id:chain] 3d5c:A (&rarr PDB)
Source: Information STRUCTURAL BASIS FOR TRANSLATION TERMINATION ON THE 70S RIBOSOME. THIS FILE CONTAINS THE 30S SUBUNIT, RELEASE FACTOR 1 (RF1), TWO TRNA, AND MRNA MOLECULES OF THE SECOND 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AS DESCRIBED IN REMARK 400.
Source: Compound 16S RRNA
Source: Resolution 3.21 ANGSTROMS.
Position (400, 424), (407, 418)
Primary structure ('_': anchors) _GAAGAA_-_GUAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C4'-exo, 4: C1'-exo, 5: C1'-exo, 6: C2'-exo, 8: C2'-exo, 9: C4'-exo, 10: C3'-exo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		4: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 11 &larr
3 3 5 ↑
4 6 7 ↑
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 13 O2'/Watson-Crick ?
3 2 14 Hoogsteen/Sugar trans y
4 3 12 Hoogsteen/Watson-Crick trans y
5 5 10 Bifurcated/O2' trans
6 5 11 O2'/Bifurcated ?
7 6 10 Bifurcated/O2' ?
8 6 12 Watson-Crick/Hoogsteen trans
9 7 10 Hoogsteen/Hoogsteen trans y
10 8 9 Watson-Crick/Watson-Crick cis
11 11 13 Hoogsteen/Watson-Crick cis
12 14 15 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters