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
CGGGAG*CAG
Length
9 nucleotides
Bulged bases
5NDJ|1|13|G|2071
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
IL_5NDJ_062 not in the Motif Atlas
Homologous match to IL_4LFB_064
Geometric discrepancy: 0.419
The information below is about IL_4LFB_064
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
IL_49061.1
Basepair signature
cWW-L-R-L-cWW-L
Number of instances in this motif group
6

Unit IDs

5NDJ|1|13|C|2068
5NDJ|1|13|G|2069
5NDJ|1|13|G|2070
5NDJ|1|13|G|2071
5NDJ|1|13|A|2072
5NDJ|1|13|G|2073
*
5NDJ|1|13|C|2082
5NDJ|1|13|A|2083
5NDJ|1|13|G|2084

Current chains

Chain 13
16S ribosomal RNA

Nearby chains

Chain 1H
Large subunit ribosomal RNA; LSU rRNA
Chain B8
50S ribosomal protein L19
Chain BI
30S ribosomal protein S20

Coloring options:


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