Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-2-0-2-10-12-Multiloop pdb2gya10.m1954-2300
Source: [PDB-id:chain] 2gya:0 (&rarr PDB)
Source: Information STRUCTURE OF THE 50S SUBUNIT OF A PRE-TRANSLOCATIONAL E. COLI RIBOSOME OBTAINED BY FITTING ATOMIC MODELS FOR RNA AND PROTEIN COMPONENTS INTO CRYO-EM MAP EMD-1056
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.00 ANGSTROMS.
Position (1955, 2299), (1960, 2114), (2117, 2129), (2130, 2152), (2155, 2250), (2261, 2286)
Primary structure ('_': anchors) _CUUU_-_UU_-__-_GC_-_CAUAGUGAUC_-_UCAACGGAAAAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		36: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		36: syn, 37: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 6 40 →
4 7 8 ↑
5 8 9 ↑
6 10 33 →
7 13 14 ↑
8 15 16 ↑
9 15 22 ↓
10 19 20 ↑
11 24 31 &larr
12 25 26 ↑
13 25 36 ↓
14 26 27 ↑
15 27 28 ↑
16 30 31 ↑
17 40 41 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 42 Watson-Crick/Watson-Crick cis y
2 6 7 Watson-Crick/Watson-Crick cis y
3 6 39 O2'/Sugar ?
4 7 39 Watson-Crick/O2' ?
5 8 40 Hoogsteen/Watson-Crick cis
6 10 11 Watson-Crick/Watson-Crick cis y
7 12 13 Watson-Crick/Watson-Crick cis
8 14 34 Watson-Crick/Watson-Crick cis
9 16 17 Watson-Crick/Watson-Crick cis
10 24 32 O2'/Bifurcated ?
11 24 36 Bifurcated/O2' trans y
12 25 31 Watson-Crick/Hoogsteen trans y
13 28 29 Watson-Crick/Watson-Crick cis
14 32 34 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters