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
CGAUGG*UGUUGACG
Length
14 nucleotides
Bulged bases
5NDG|1|5|U|2159, 5NDG|1|5|U|2175, 5NDG|1|5|C|2179
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_310 not in the Motif Atlas
Homologous match to IL_5TBW_083
Geometric discrepancy: 0.0736
The information below is about IL_5TBW_083
Detailed Annotation
Kink-turn related
Broad Annotation
No text annotation
Motif group
IL_64509.1
Basepair signature
cWW-tWW-tWW-tSS-L-cWW
Number of instances in this motif group
2

Unit IDs

5NDG|1|5|C|2156
5NDG|1|5|G|2157
5NDG|1|5|A|2158
5NDG|1|5|U|2159
5NDG|1|5|G|2160
5NDG|1|5|G|2161
*
5NDG|1|5|U|2173
5NDG|1|5|G|2174
5NDG|1|5|U|2175
5NDG|1|5|U|2176
5NDG|1|5|G|2177
5NDG|1|5|A|2178
5NDG|1|5|C|2179
5NDG|1|5|G|2180

Current chains

Chain 5
25S ribosomal RNA

Nearby chains

Chain 6
Small subunit ribosomal RNA; SSU rRNA
Chain l2
60S ribosomal protein L2-A
Chain q3
60S ribosomal protein L43-A

Coloring options:


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