IL_5NDJ_253

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

GGA*UAACC

Length

8 nucleotides

Bulged bases

5NDJ|1|1H|G|825, 5NDJ|1|1H|A|837, 5NDJ|1|1H|A|838, 5NDJ|1|1H|C|839

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_253 not in the Motif Atlas

Geometric match to IL_7RQB_023

Geometric discrepancy: 0.0826

The information below is about IL_7RQB_023

Detailed Annotation

Multiple bulged bases

Broad Annotation

No text annotation

Motif group

IL_90991.6

Basepair signature

cWW-cWW

Number of instances in this motif group

7

Unit IDs

5NDJ|1|1H|G|824
5NDJ|1|1H|G|825
5NDJ|1|1H|A|826
*
5NDJ|1|1H|U|836
5NDJ|1|1H|A|837
5NDJ|1|1H|A|838
5NDJ|1|1H|C|839
5NDJ|1|1H|C|840

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L2

Chain 31

50S ribosomal protein L4

Chain E8

50S ribosomal protein L22

Chain P8

50S ribosomal protein L34