J4_5NDJ_035

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

AUAG*CAG*CGUGUCC*GU

Length

16 nucleotides

Bulged bases

5NDJ|1|V4|U|45, 5NDJ|1|V4|U|47

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

J4_5NDJ_035 not in the Motif Atlas

Homologous match to J4_2CSX_001

Geometric discrepancy: 0.5994

The information below is about J4_2CSX_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_36296.3

Basepair signature

cWW-F-cWW-cWW-F-F-F-cWW

Number of instances in this motif group

5

Unit IDs

5NDJ|1|V4|A|7
5NDJ|1|V4|U|8
5NDJ|1|V4|A|9
5NDJ|1|V4|G|10
*
5NDJ|1|V4|C|25
5NDJ|1|V4|A|26
5NDJ|1|V4|G|27
*
5NDJ|1|V4|C|43
5NDJ|1|V4|G|44
5NDJ|1|V4|U|45
5NDJ|1|V4|G|46
5NDJ|1|V4|U|47
5NDJ|1|V4|C|48
5NDJ|1|V4|C|49
*
5NDJ|1|V4|G|65
5NDJ|1|V4|U|66

Current chains

Chain V4

tRNA-Phe

Nearby chains

Chain 2A

30S ribosomal protein S11

Chain 62

30S ribosomal protein S7