Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'25-Hairpin pdb2vhp1A.e678-704
Source: [PDB-id:chain] 2vhp:A (&rarr PDB)
Source: Information STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME (PART 4 OF 4)
Source: Compound 16S RIBOSOMAL RNA
Source: Resolution 3.74 ANGSTROMS.
Position (678, 704)
Primary structure ('_': anchors) _GUGUAGCGGUGAAAUGCGUAGAGAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-exo, 2: C4'-exo, 5: C3'-exo, 6: C2'-endo, 7: C2'-exo, 8: C2'-exo, 12: C2'-exo, 14: C2'-exo, 15: C2'-exo, 19: C2'-exo, 20: C2'-endo, 21: C2'-endo, 22: C3'-exo, 24: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 6: syn, 20: syn, 22: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 3 ↑
2 3 4 ↑
3 7 8 ↑
4 7 19 →
5 12 13 ↑
6 13 14 ↑
7 14 15 ↑
8 15 16 ↑
9 16 17 ↑
10 17 18 ↑
11 24 25 ↑
12 25 26 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 27 Watson-Crick/Watson-Crick cis
2 3 26 Watson-Crick/Watson-Crick cis y
3 6 22 Sugar/Hoogsteen trans
4 7 23 Bifurcated/O2' trans y
5 10 15 Bifurcated/O2' trans
6 11 13 Hoogsteen/O2' ?
7 11 14 O2'/Watson-Crick ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters