J4_5NDK_025
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
- UUG*CG*CCUAAGGUAG*CGAAAA
- Length
- 21 nucleotides
- Bulged bases
- 5NDK|1|1H|A|1996
- 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_025 not in the Motif Atlas
- Homologous match to J4_9DFE_008
- Geometric discrepancy: 0.061
- The information below is about J4_9DFE_008
- Detailed Annotation
- No text annotation
- Broad Annotation
- No text annotation
- Motif group
- J4_42306.1
- Basepair signature
- cWW-tSS-cSS-cWH-cWW-tWH-tHS-cWW-cWW-tWW-F-cSH-F-F
- Number of instances in this motif group
- 5
Unit IDs
5NDK|1|1H|U|1867
5NDK|1|1H|U|1868
5NDK|1|1H|G|1869
*
5NDK|1|1H|C|1930
5NDK|1|1H|G|1931
*
5NDK|1|1H|C|1949
5NDK|1|1H|C|1950
5NDK|1|1H|U|1951
5NDK|1|1H|A|1952
5NDK|1|1H|A|1953
5NDK|1|1H|G|1954
5NDK|1|1H|G|1955
5NDK|1|1H|U|1956
5NDK|1|1H|A|1957
5NDK|1|1H|G|1958
*
5NDK|1|1H|C|1992
5NDK|1|1H|G|1993
5NDK|1|1H|A|1994
5NDK|1|1H|A|1995
5NDK|1|1H|A|1996
5NDK|1|1H|A|1997
Current chains
- Chain 1H
- 23S ribosomal RNA
Nearby chains
- Chain 11
- 50S ribosomal protein L2
- Chain 13
- Small subunit ribosomal RNA; SSU rRNA
- Chain X1
- Transfer RNA; tRNA
Coloring options: