IL_5NDJ_047

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

CCAGC*GG

Length

7 nucleotides

Bulged bases

None detected

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_047 not in the Motif Atlas

Homologous match to IL_5J7L_052

Geometric discrepancy: 0.4765

The information below is about IL_5J7L_052

Detailed Annotation

Minor groove platform

Broad Annotation

No text annotation

Motif group

IL_15052.4

Basepair signature

cWW-L-cWW-L

Number of instances in this motif group

8

Unit IDs

5NDJ|1|13|C|1756
5NDJ|1|13|C|1757
5NDJ|1|13|A|1758
5NDJ|1|13|G|1759
5NDJ|1|13|C|1760
*
5NDJ|1|13|G|1770
5NDJ|1|13|G|1771

Current chains

Chain 13

16S ribosomal RNA

Nearby chains

Chain 8E

30S ribosomal protein S9