Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-7-Internal Loop pdb1s1i13.n1939-1948
Source: [PDB-id:chain] 1s1i:3 (&rarr PDB)
Source: Information STRUCTURE OF THE RIBOSOMAL 80S-EEF2-SORDARIN COMPLEX FROM YEAST OBTAINED BY DOCKING ATOMIC MODELS FOR RNA AND PROTEIN COMPONENTS INTO A 11.7 A CRYO-EM MAP. THIS FILE, 1S1I, CONTAINS 60S SUBUNIT. THE 40S RIBOSOMAL SUBUNIT IS IN FILE 1S1H.
Source: Compound 5.8S/25S RIBOSOMAL RNAILS: REPRESENTED BY THE ANALOGOUS MOLECULE OF H.
Source: Resolution 1.70 ANGSTROMS.
Position (1933, 1956), (1939, 1948)
Primary structure ('_': anchors) _GCAAA_-_CUCGUAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 3: C4'-exo, 4: C2'-endo, 10: C2'-endo, 11: C2'-endo, 13: C2'-endo, 14: C2'-endo, 15: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		2: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 14 ↓
2 3 5 →
3 5 6 ↑
4 6 7 ↑
5 8 9 ↑
6 9 10 &larr
7 10 12 →
8 12 13 ↑
9 14 16 →
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 5 Sugar/O2' ?
2 1 16 Watson-Crick/Watson-Crick cis
3 2 13 O2'/Bifurcated ?
4 2 14 O2'/Bifurcated ?
5 3 12 Watson-Crick/Watson-Crick trans
6 3 14 Hoogsteen/Hoogsteen trans y
7 5 10 Hoogsteen/Hoogsteen trans y
8 6 9 Watson-Crick/Watson-Crick cis y
9 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters