Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-8-Internal Loop pdb2gycF9.n16-57
Source: [PDB-id:chain] 2gyc:9 (&rarr PDB)
Source: Information STRUCTURE OF THE 50S SUBUNIT OF A SECM-STALLED E. COLI RIBOSOME COMPLEX OBTAINED BY FITTING ATOMIC MODELS FOR RNA AND PROTEIN COMPONENTS INTO CRYO-EM MAP EMD-1143
Source: Compound 5S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 2.00 ANGSTROMS.
Position (18, 55), (27, 45)
Primary structure ('_': anchors) _GAAGUGAAA_-_GUCCCACC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		None
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 5 6 ↑
3 6 7 ↑
4 7 8 ↑
5 10 11 ↑
6 12 13 ↑
7 13 14 ↑
8 14 15 ↑
9 16 17 ↑
10 17 18 ↑
11 20 21 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 21 Watson-Crick/Watson-Crick cis y
2 2 17 Watson-Crick/Watson-Crick cis y
3 4 14 Watson-Crick/O2' ?
4 5 16 Bifurcated/Watson-Crick cis y
5 7 14 Watson-Crick/Watson-Crick cis
6 8 9 Hoogsteen/O2' ?
7 8 13 Watson-Crick/O2' trans y
8 11 12 Watson-Crick/Watson-Crick cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters