IL_5NDJ_248

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

GAAAC*GAGAUAGC

Length

13 nucleotides

Bulged bases

5NDJ|1|1H|G|850, 5NDJ|1|1H|G|854

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_248 not in the Motif Atlas

Geometric match to IL_4WF9_021

Geometric discrepancy: 0.0815

The information below is about IL_4WF9_021

Detailed Annotation

tHW-tHW cross-strand stack

Broad Annotation

No text annotation

Motif group

IL_54041.2

Basepair signature

cWW-L-R-L-R-tWH-L-cWW

Number of instances in this motif group

7

Unit IDs

5NDJ|1|1H|G|723
5NDJ|1|1H|A|724
5NDJ|1|1H|A|725
5NDJ|1|1H|A|726
5NDJ|1|1H|C|727
*
5NDJ|1|1H|G|848
5NDJ|1|1H|A|849
5NDJ|1|1H|G|850
5NDJ|1|1H|A|851
5NDJ|1|1H|U|852
5NDJ|1|1H|A|853
5NDJ|1|1H|G|854
5NDJ|1|1H|C|855

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 31

50S ribosomal protein L4

Chain 78

50S ribosomal protein L15