Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb2vhm1B.n2402-2443
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 (2403, 2442), (2408, 2436)
Primary structure ('_': anchors) _UGAU_-_GUUUG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C1'-exo, 5: C2'-exo, 8: C3'-exo, 9: C2'-endo, 12: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn, 9: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 8 ↓
2 4 5 ↑
3 5 6 ↑
4 7 8 ↑
5 10 11 ↑
6 11 12 ↑
7 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis y
2 3 5 Watson-Crick/C trans y
3 3 8 Bifurcated/O2' ?
4 4 11 Watson-Crick/Watson-Crick cis
5 5 10 Watson-Crick/Watson-Crick cis
6 6 7 Watson-Crick/Watson-Crick cis
7 7 9 Hoogsteen/Watson-Crick trans y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters