IL_5NDK_237

3D structure

PDB id

5NDK (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA

Experimental method

X-RAY DIFFRACTION

Resolution

2.95 Å

Loop

Sequence

GGGAG*CGUGGAUC

Length

13 nucleotides

Bulged bases

5NDK|1|1H|G|99

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_5NDK_237 not in the Motif Atlas

Homologous match to IL_7RQB_004

Geometric discrepancy: 0.0537

The information below is about IL_7RQB_004

Detailed Annotation

Kink-turn

Broad Annotation

No text annotation

Motif group

IL_45067.2

Basepair signature

cWW-tSS-L-tSH-L-R-R-cWW-L

Number of instances in this motif group

18

Unit IDs

5NDK|1|1H|G|80
5NDK|1|1H|G|81
5NDK|1|1H|G|82
5NDK|1|1H|A|83
5NDK|1|1H|G|84
*
5NDK|1|1H|C|96
5NDK|1|1H|G|97
5NDK|1|1H|U|98
5NDK|1|1H|G|99
5NDK|1|1H|G|100
5NDK|1|1H|A|101
5NDK|1|1H|U|102
5NDK|1|1H|C|103

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain G8

50S ribosomal protein L24

Chain K8

50S ribosomal protein L29