IL_5NDJ_059

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

GGAG*UGAC

Length

8 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_059 not in the Motif Atlas

Homologous match to IL_5J7L_062

Geometric discrepancy: 0.0861

The information below is about IL_5J7L_062

Detailed Annotation

Double sheared

Broad Annotation

Double sheared

Motif group

IL_09705.15

Basepair signature

cWW-tSH-tHS-cWW

Number of instances in this motif group

34

Unit IDs

5NDJ|1|13|G|2044
5NDJ|1|13|G|2045
5NDJ|1|13|A|2046
5NDJ|1|13|G|2047
*
5NDJ|1|13|U|2104
5NDJ|1|13|G|2105
5NDJ|1|13|A|2106
5NDJ|1|13|C|2107

Current chains

Chain 13

16S ribosomal RNA

Nearby chains

Chain 1H

Large subunit ribosomal RNA; LSU rRNA

Chain 3I

30S ribosomal protein S12