J5_5NDG_009
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
- AGG*CGAUGAAG*UGAACG*CG*CAU
- Length
- 22 nucleotides
- Bulged bases
- 5NDG|1|8|U|38
- 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_009 not in the Motif Atlas
- Homologous match to J5_8P9A_010
- Geometric discrepancy: 0.0701
- The information below is about J5_8P9A_010
- Detailed Annotation
- No text annotation
- Broad Annotation
- No text annotation
- Motif group
- J5_01737.2
- Basepair signature
- cWW-F-cWW-F-cWW-tSH-tHH-tHS-cWW-cWW-cWW-F
- Number of instances in this motif group
- 5
Unit IDs
5NDG|1|5|A|20
5NDG|1|5|G|21
5NDG|1|5|G|22
*
5NDG|1|8|C|35
5NDG|1|8|G|36
5NDG|1|8|A|37
5NDG|1|8|U|38
5NDG|1|8|G|39
5NDG|1|8|A|40
5NDG|1|8|A|41
5NDG|1|8|G|42
*
5NDG|1|8|U|102
5NDG|1|8|G|103
5NDG|1|8|A|104
5NDG|1|8|A|105
5NDG|1|8|C|106
5NDG|1|8|G|107
*
5NDG|1|8|C|115
5NDG|1|8|G|116
*
5NDG|1|8|C|137
5NDG|1|8|A|138
5NDG|1|8|U|139
Current chains
- Chain 5
- 25S ribosomal RNA
- Chain 8
- 5.8S ribosomal RNA
Nearby chains
- Chain m5
- 60S ribosomal protein L15-A
- Chain n5
- 60S ribosomal protein L25
- Chain o5
- 60S ribosomal protein L35-A
- Chain o7
- 60S ribosomal protein L37-A
- Chain o9
- 60S ribosomal protein L39
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