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
AUAG*CAG*CGUGUCC*GU
Length
16 nucleotides
Bulged bases
5NDJ|1|W1|U|8, 5NDJ|1|W1|U|47, 5NDJ|1|W1|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_5NDJ_030 not in the Motif Atlas
Homologous match to J4_6CFJ_015
Geometric discrepancy: 0.3956
The information below is about J4_6CFJ_015
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J4_70449.29
Basepair signature
cWW-F-cWW-cWW-cHS-F-cWW-cWW
Number of instances in this motif group
54

Unit IDs

5NDJ|1|W1|A|7
5NDJ|1|W1|U|8
5NDJ|1|W1|A|9
5NDJ|1|W1|G|10
*
5NDJ|1|W1|C|25
5NDJ|1|W1|A|26
5NDJ|1|W1|G|27
*
5NDJ|1|W1|C|43
5NDJ|1|W1|G|44
5NDJ|1|W1|U|45
5NDJ|1|W1|G|46
5NDJ|1|W1|U|47
5NDJ|1|W1|C|48
5NDJ|1|W1|C|49
*
5NDJ|1|W1|G|65
5NDJ|1|W1|U|66

Current chains

Chain W1
tRNA-Phe

Nearby chains

Chain 1H
Large subunit ribosomal RNA; LSU rRNA

Coloring options:


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