IL_5NDJ_044

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

CG*CUG

Length

5 nucleotides

Bulged bases

5NDJ|1|13|U|1823

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_044 not in the Motif Atlas

Homologous match to IL_4LFB_046

Geometric discrepancy: 0.1106

The information below is about IL_4LFB_046

Detailed Annotation

Single bulged U

Broad Annotation

No text annotation

Motif group

IL_89505.4

Basepair signature

cWW-L-cWW

Number of instances in this motif group

117

Unit IDs

5NDJ|1|13|C|1688
5NDJ|1|13|G|1689
*
5NDJ|1|13|C|1822
5NDJ|1|13|U|1823
5NDJ|1|13|G|1824

Current chains

Chain 13

16S ribosomal RNA

Nearby chains

Chain 1I

30S ribosomal protein S10

Chain 2E

30S ribosomal protein S3

Chain 4E

30S ribosomal protein S5

Chain 5I

30S ribosomal protein S14 type Z

Chain 8E

30S ribosomal protein S9

Chain W1

Transfer RNA; tRNA

Chain Y1

mRNA