J5_5NDG_002
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
- GGAGUC*GGAC*GUUC*GC*GCAGAUC
- Length
- 23 nucleotides
- Bulged bases
- 5NDG|1|1|U|1436
- 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
- J5_5NDG_002 not in the Motif Atlas
- Homologous match to J5_8P9A_011
- Geometric discrepancy: 0.0647
- The information below is about J5_8P9A_011
- Detailed Annotation
- No text annotation
- Broad Annotation
- No text annotation
- Motif group
- J5_63811.1
- Basepair signature
- cWW-tSH-tSS-tHW-F-cWS-F-tWS-cWW-cWW-F-cWW-cWW-F
- Number of instances in this motif group
- 2
Unit IDs
5NDG|1|1|G|658
5NDG|1|1|G|659
5NDG|1|1|A|660
5NDG|1|1|G|661
5NDG|1|1|U|662
5NDG|1|1|C|663
*
5NDG|1|1|G|799
5NDG|1|1|G|800
5NDG|1|1|A|801
5NDG|1|1|C|802
*
5NDG|1|1|G|941
5NDG|1|1|U|942
5NDG|1|1|U|943
5NDG|1|1|C|944
*
5NDG|1|1|G|1375
5NDG|1|1|C|1376
*
5NDG|1|1|G|1431
5NDG|1|1|C|1432
5NDG|1|1|A|1433
5NDG|1|1|G|1434
5NDG|1|1|A|1435
5NDG|1|1|U|1436
5NDG|1|1|C|1437
Current chains
- Chain 1
- 25S ribosomal RNA
Nearby chains
- Chain 4
- 5.8S ribosomal RNA; 5.8S rRNA
- Chain L4
- 60S ribosomal protein L4-A
- Chain M3
- 60S ribosomal protein L13-A
- Chain M5
- 60S ribosomal protein L15-A
- Chain N8
- 60S ribosomal protein L28
- Chain O2
- 60S ribosomal protein L32
Coloring options: