3D structure

PDB id
5NDJ (explore in PDB, NAKB, or RNA 3D Hub)
Description
Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)
Experimental method
X-RAY DIFFRACTION
Resolution
3.15 Å

Loop

Sequence
CAAUG*CCCAGUUC*GCCG
Length
17 nucleotides
Bulged bases
5NDJ|1|1G|U|1867
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
J3_5NDJ_039 not in the Motif Atlas
Homologous match to J3_4LFB_009
Geometric discrepancy: 0.1273
The information below is about J3_4LFB_009
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J3_37047.6
Basepair signature
cWW-cSS-tHW-F-F-F-cWW-cWW-F-cSH-F-F
Number of instances in this motif group
4

Unit IDs

5NDJ|1|1G|C|1864
5NDJ|1|1G|A|1865
5NDJ|1|1G|A|1866
5NDJ|1|1G|U|1867
5NDJ|1|1G|G|1868
*
5NDJ|1|1G|C|1923
5NDJ|1|1G|C|1924
5NDJ|1|1G|C|1925
5NDJ|1|1G|A|1926
5NDJ|1|1G|G|1927
5NDJ|1|1G|U|1928
5NDJ|1|1G|U|1929
5NDJ|1|1G|C|1930
*
5NDJ|1|1G|G|1961
5NDJ|1|1G|C|1962
5NDJ|1|1G|C|1963
5NDJ|1|1G|G|1964

Current chains

Chain 1G
16S ribosomal RNA

Nearby chains

Chain 1B
30S ribosomal protein Thx
Chain 4A
30S ribosomal protein S13
Chain 62
30S ribosomal protein S7

Coloring options:


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