IL_5NDJ_139

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

CAG*CGGG

Length

7 nucleotides

Bulged bases

5NDJ|1|14|G|2253

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_139 not in the Motif Atlas

Homologous match to IL_7RQB_082

Geometric discrepancy: 0.0672

The information below is about IL_7RQB_082

Detailed Annotation

Isolated tHS basepair with bulges

Broad Annotation

No text annotation

Motif group

IL_38958.7

Basepair signature

cWW-tHS-cWW

Number of instances in this motif group

15

Unit IDs

5NDJ|1|14|C|2106
5NDJ|1|14|A|2107
5NDJ|1|14|G|2108
*
5NDJ|1|14|C|2251
5NDJ|1|14|G|2252
5NDJ|1|14|G|2253
5NDJ|1|14|G|2254

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 19

50S ribosomal protein L2

Chain F5

50S ribosomal protein L28

Chain V4

Transfer RNA; tRNA