IL_5NDJ_307

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

GA*UACC

Length

6 nucleotides

Bulged bases

5NDJ|1|1H|A|2454

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_307 not in the Motif Atlas

Homologous match to IL_7RQB_081

Geometric discrepancy: 0.085

The information below is about IL_7RQB_081

Detailed Annotation

Minor groove platform

Broad Annotation

No text annotation

Motif group

IL_42622.4

Basepair signature

cWW-cSH-cWW

Number of instances in this motif group

33

Unit IDs

5NDJ|1|1H|G|2095
5NDJ|1|1H|A|2096
*
5NDJ|1|1H|U|2453
5NDJ|1|1H|A|2454
5NDJ|1|1H|C|2455
5NDJ|1|1H|C|2456

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L2

Chain X1

Transfer RNA; tRNA