3D structure

PDB id
5NDG (explore in PDB, NAKB, or RNA 3D Hub)
Description
Crystal structure of geneticin (G418) bound to the yeast 80S ribosome
Experimental method
X-RAY DIFFRACTION
Resolution
3.7 Å

Loop

Sequence
UCUAGACAG*CCGAA
Length
14 nucleotides
Bulged bases
5NDG|1|5|A|1221
QA status
Valid loop

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.
R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.
R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.
R3DMCS Rfam
IL_5NDG_281 not in the Motif Atlas
Homologous match to IL_8C3A_057
Geometric discrepancy: 0.2
The information below is about IL_8C3A_057
Detailed Annotation
Kink-turn
Broad Annotation
No text annotation
Motif group
IL_90538.5
Basepair signature
cWW-tSS-tSS-tSH-L-tHS-R-cWW-L-L
Number of instances in this motif group
6

Unit IDs

5NDG|1|5|U|1218
5NDG|1|5|C|1219
5NDG|1|5|U|1220
5NDG|1|5|A|1221
5NDG|1|5|G|1222
5NDG|1|5|A|1223
5NDG|1|5|C|1224
5NDG|1|5|A|1225
5NDG|1|5|G|1226
*
5NDG|1|5|C|1283
5NDG|1|5|C|1284
5NDG|1|5|G|1285
5NDG|1|5|A|1286
5NDG|1|5|A|1287

Current chains

Chain 5
25S ribosomal RNA

Nearby chains

Chain l9
60S ribosomal protein L9-A
Chain n0
60S ribosomal protein L20-A
Chain p0
60S acidic ribosomal protein P0

Coloring options:


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