Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-8-11-7-4-Multiloop pdb1vqm10.m2059-2510
Source: [PDB-id:chain] 1vqm:0 (&rarr PDB)
Source: Information THE STRUCTURE OF THE TRANSITION STATE ANALOGUE "DAN" BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.30 ANGSTROMS.
Position (2060, 2509), (2067, 2344), (2353, 2394), (2406, 2478), (2486, 2504)
Primary structure ('_': anchors) _GAAGAC_-_GAUAACAG_-_ACCUCGAUGUC_-_GGGUUUA_-_GGCU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-endo, 5: C2'-endo, 6: C3'-exo, 10: C2'-endo, 11: C2'-endo, 12: C2'-endo, 20: C3'-exo, 21: C2'-exo, 24: O4'-endo, 25: C4'-exo, 26: C2'-endo, 27: C2'-endo, 33: C2'-endo, 37: C2'-endo, 44: C2'-endo, 45: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		26: syn, 33: syn, 44: syn, 45: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 26 ↑
3 4 25 →
4 5 7 ↑
5 5 26 ↓
6 7 8 ↑
7 9 24 &larr
8 10 23 &larr
9 10 24 →
10 13 14 ↑
11 15 16 ↑
12 16 17 ↑
13 17 18 ↑
14 19 20 ↑
15 22 23 ↑
16 30 31 ↑
17 30 35 →
18 32 33 &larr
19 33 45 ↓
20 34 35 ↑
21 35 36 ↑
22 38 39 →
23 40 42 →
24 41 42 ↑
25 42 43 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 46 Watson-Crick/Watson-Crick cis
2 5 7 Bifurcated/O2' ?
3 5 14 Watson-Crick/Watson-Crick cis
4 6 26 Watson-Crick/Hoogsteen cis y
5 7 13 Watson-Crick/Watson-Crick cis y
6 8 9 Watson-Crick/Watson-Crick cis
7 9 12 Watson-Crick/Sugar trans y
8 10 13 O2'/Bifurcated ?
9 10 14 Hoogsteen/Watson-Crick cis y
10 13 24 Watson-Crick/Hoogsteen trans
11 14 20 Bifurcated/O2' ?
12 17 21 Watson-Crick/Watson-Crick cis
13 18 19 Watson-Crick/Watson-Crick cis
14 20 21 Hoogsteen/Sugar cis y
15 30 34 Watson-Crick/Watson-Crick cis
16 31 32 Watson-Crick/Watson-Crick cis
17 38 43 Bifurcated/O2' ?
18 39 43 O2'/Bifurcated trans
19 40 41 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters