Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-5-Internal Loop pdb2vhm1B.n1464-1495
Source: [PDB-id:chain] 2vhm:B (&rarr PDB)
Source: Information STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME (PART 1 OF 4)
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.74 ANGSTROMS.
Position (1458, 1501), (1464, 1495)
Primary structure ('_': anchors) _GUAGG_-_CUGAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 3: C2'-exo, 5: C2'-exo, 6: C2'-exo, 9: C2'-exo, 11: C2'-exo, 12: C4'-exo, 13: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 13 →
2 4 5 ↑
3 4 12 →
4 5 6 ↑
5 5 11 →
6 6 7 ↑
7 8 9 ↑
8 9 10 ↑
9 10 11 ↑
10 12 13 ↑
11 13 14 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 3 11 Watson-Crick/O2' ?
3 3 12 Hoogsteen/Watson-Crick trans
4 4 5 Hoogsteen/O2' ?
5 4 11 O2'/Bifurcated trans y
6 5 10 Watson-Crick/Watson-Crick cis y
7 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters