J4_5NDK_033
3D structure
- PDB id
- 5NDK (explore in PDB, NAKB, or RNA 3D Hub)
- Description
- Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA
- Experimental method
- X-RAY DIFFRACTION
- Resolution
- 2.95 Å
Loop
- Sequence
- AUAG*CAG*CGUGUCC*GU
- Length
- 16 nucleotides
- Bulged bases
- 5NDK|1|X4|U|8, 5NDK|1|X4|U|47, 5NDK|1|X4|C|48
- 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_5NDK_033 not in the Motif Atlas
- Homologous match to J4_6UFM_001
- Geometric discrepancy: 0.2073
- The information below is about J4_6UFM_001
- Detailed Annotation
- tRNA junction
- Broad Annotation
- No text annotation
- Motif group
- J4_95067.1
- Basepair signature
- cWW-F-cWW-cWW-cHS-F-cWW-cWW
- Number of instances in this motif group
- 48
Unit IDs
5NDK|1|X4|A|7
5NDK|1|X4|U|8
5NDK|1|X4|A|9
5NDK|1|X4|G|10
*
5NDK|1|X4|C|25
5NDK|1|X4|A|26
5NDK|1|X4|G|27
*
5NDK|1|X4|C|43
5NDK|1|X4|G|44
5NDK|1|X4|U|45
5NDK|1|X4|G|46
5NDK|1|X4|U|47
5NDK|1|X4|C|48
5NDK|1|X4|C|49
*
5NDK|1|X4|G|65
5NDK|1|X4|U|66
Current chains
- Chain X4
- tRNA-Phe
Nearby chains
- Chain 14
- Large subunit ribosomal RNA; LSU rRNA
- Chain 45
- 50S ribosomal protein L16
- Chain 4A
- 30S ribosomal protein S13
- Chain E5
- 50S ribosomal protein L27
- Chain W4
- Transfer RNA; tRNA
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