Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-2-5-19-0-5-Multiloop pdb2vhm1B.m812-1179
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 (816, 1175), (822, 835), (838, 924), (930, 955), (975, 1147), (1148, 1169)
Primary structure ('_': anchors) _CGAAA_-_GC_-_AGACA_-_AAGAGGGAAACAACCCAGA_-__-_GGUAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-exo, 3: C2'-exo, 4: C2'-exo, 5: C2'-exo, 7: C4'-exo, 10: C2'-exo, 16: C2'-exo, 17: O4'-endo, 18: C2'-exo, 20: C4'-exo, 21: C2'-endo, 22: C1'-exo, 23: C2'-exo, 24: C2'-exo, 25: C2'-exo, 26: C4'-exo, 27: C4'-exo, 30: O4'-endo, 31: C4'-exo, 32: C3'-exo, 33: C2'-exo, 34: C2'-exo, 36: C2'-exo, 37: C4'-exo, 38: C1'-endo, 39: C2'-exo, 44: C2'-exo, 46: C2'-exo, 47: C2'-exo, 48: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		22: syn, 30: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 3 ↑
2 4 5 ↑
3 4 46 →
4 5 6 ↑
5 6 18 ↑
6 7 9 →
7 8 9 ↑
8 9 10 ↑
9 12 13 ↑
10 13 14 ↑
11 14 15 ↑
12 15 16 ↑
13 19 20 ↑
14 20 21 &larr
15 21 45 →
16 22 37 ↓
17 22 43 ↑
18 23 24 ↑
19 23 38 →
20 24 25 ↑
21 25 26 ↑
22 26 34 →
23 28 29 ↑
24 31 32 ↑
25 34 35 ↑
26 35 36 ↑
27 39 42 ↓
28 40 41 ↑
29 43 44 ↑
30 46 47 ↑
31 47 48 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 48 Watson-Crick/Watson-Crick cis
2 3 45 O2'/Bifurcated ?
3 4 44 Bifurcated/O2' ?
4 4 45 Watson-Crick/Hoogsteen trans
5 5 9 Bifurcated/O2' ?
6 5 15 O2'/Sugar ?
7 5 21 Bifurcated/O2' trans
8 6 20 Sugar/Hoogsteen trans y
9 7 8 Watson-Crick/Watson-Crick cis
10 7 15 Bifurcated/Hoogsteen cis y
11 10 14 Watson-Crick/Watson-Crick cis
12 11 12 Watson-Crick/Watson-Crick cis
13 13 47 O2'/Sugar ?
14 14 46 Sugar/O2' ?
15 18 19 Watson-Crick/Watson-Crick cis
16 19 22 Bifurcated/O2' ?
17 19 31 Sugar/O2' ?
18 22 43 Bifurcated/O2' ?
19 23 37 Sugar/Hoogsteen trans y
20 24 35 Watson-Crick/Watson-Crick cis y
21 28 30 Bifurcated/O2' ?
22 32 33 Bifurcated/O2' ?
23 38 43 O2'/Bifurcated ?
24 39 40 Watson-Crick/Watson-Crick cis
25 41 42 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters