J3_5NDG_060
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
- CGAUAGCGAACAAGUAC*GGAAAG*CUUG
- Length
- 27 nucleotides
- Bulged bases
- 5NDG|1|1|U|343, 5NDG|1|1|A|351, 5NDG|1|4|U|23
- 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
- J3_5NDG_060 not in the Motif Atlas
- Homologous match to J3_8P9A_045
- Geometric discrepancy: 0.0526
- The information below is about J3_8P9A_045
- Detailed Annotation
- No text annotation
- Broad Annotation
- No text annotation
- Motif group
- J3_30040.2
- Basepair signature
- cWW-tWH-F-cWW-tSS-tHH-cSS-tWH-tSW-tHS-cWW-tWH-F-cSH-tSS-F-F
- Number of instances in this motif group
- 7
Unit IDs
5NDG|1|1|C|340
5NDG|1|1|G|341
5NDG|1|1|A|342
5NDG|1|1|U|343
5NDG|1|1|A|344
5NDG|1|1|G|345
5NDG|1|1|C|346
5NDG|1|1|G|347
5NDG|1|1|A|348
5NDG|1|1|A|349
5NDG|1|1|C|350
5NDG|1|1|A|351
5NDG|1|1|A|352
5NDG|1|1|G|353
5NDG|1|1|U|354
5NDG|1|1|A|355
5NDG|1|1|C|356
*
5NDG|1|1|G|363
5NDG|1|1|G|364
5NDG|1|1|A|365
5NDG|1|1|A|366
5NDG|1|1|A|367
5NDG|1|1|G|368
*
5NDG|1|4|C|21
5NDG|1|4|U|22
5NDG|1|4|U|23
5NDG|1|4|G|24
Current chains
- Chain 1
- 25S ribosomal RNA
- Chain 4
- 5.8S ribosomal RNA
Nearby chains
- Chain L4
- 60S ribosomal protein L4-A
- Chain N6
- 60S ribosomal protein L26-A
- Chain O7
- 60S ribosomal protein L37-A
- Chain O9
- 60S ribosomal protein L39
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