J4_5NDG_025
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
- AAG*CGAAAG*CCAUAAACUAUG*UU
- Length
- 23 nucleotides
- Bulged bases
- 5NDG|1|6|A|623, 5NDG|1|6|A|1026, 5NDG|1|6|C|1028, 5NDG|1|6|U|1029, 5NDG|1|6|A|1030, 5NDG|1|6|U|1031
- 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
- J4_5NDG_025 not in the Motif Atlas
- Homologous match to J4_8P9A_022
- Geometric discrepancy: 0.0515
- The information below is about J4_8P9A_022
- Detailed Annotation
- No text annotation
- Broad Annotation
- No text annotation
- Motif group
- J4_61885.6
- Basepair signature
- cWW-cWW-cWW-F-F-tHW-F-F-F-F-F-cWW-F-F
- Number of instances in this motif group
- 4
Unit IDs
5NDG|1|6|A|622
5NDG|1|6|A|623
5NDG|1|6|G|624
*
5NDG|1|6|C|975
5NDG|1|6|G|976
5NDG|1|6|A|977
5NDG|1|6|A|978
5NDG|1|6|A|979
5NDG|1|6|G|980
*
5NDG|1|6|C|1021
5NDG|1|6|C|1022
5NDG|1|6|A|1023
5NDG|1|6|U|1024
5NDG|1|6|A|1025
5NDG|1|6|A|1026
5NDG|1|6|A|1027
5NDG|1|6|C|1028
5NDG|1|6|U|1029
5NDG|1|6|A|1030
5NDG|1|6|U|1031
5NDG|1|6|G|1032
*
5NDG|1|6|U|1103
5NDG|1|6|U|1104
Current chains
- Chain 6
- 18S ribosomal RNA
Nearby chains
- Chain 5
- Large subunit ribosomal RNA; LSU rRNA
- Chain c1
- 40S ribosomal protein S11-A
- Chain c3
- 40S ribosomal protein S13
- Chain c4
- 40S ribosomal protein S14-A
- Chain d2
- 40S ribosomal protein S22-A
- Chain d3
- 40S ribosomal protein S23-A
- Chain d6
- 40S ribosomal protein S26-B
- Chain q1
- 60S ribosomal protein L41-A
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