J3_5NDJ_068

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

CUCG*CGAUAGCGCACCAGUAC*GGAAAG

Length

27 nucleotides

Bulged bases

5NDJ|1|1H|C|34, 5NDJ|1|1H|U|476, 5NDJ|1|1H|C|484

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

J3_5NDJ_068 not in the Motif Atlas

Homologous match to J3_5J7L_067

Geometric discrepancy: 0.2767

The information below is about J3_5J7L_067

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_30040.2

Basepair signature

cWW-tWH-F-cWW-tSS-tHH-cSS-tWH-tSW-tHS-cWW-tWH-F-cSH-tSS-F-F

Number of instances in this motif group

7

Unit IDs

5NDJ|1|1H|C|32
5NDJ|1|1H|U|33
5NDJ|1|1H|C|34
5NDJ|1|1H|G|35
*
5NDJ|1|1H|C|473
5NDJ|1|1H|G|474
5NDJ|1|1H|A|475
5NDJ|1|1H|U|476
5NDJ|1|1H|A|477
5NDJ|1|1H|G|478
5NDJ|1|1H|C|479
5NDJ|1|1H|G|480
5NDJ|1|1H|C|481
5NDJ|1|1H|A|482
5NDJ|1|1H|C|483
5NDJ|1|1H|C|484
5NDJ|1|1H|A|485
5NDJ|1|1H|G|486
5NDJ|1|1H|U|487
5NDJ|1|1H|A|488
5NDJ|1|1H|C|489
*
5NDJ|1|1H|G|496
5NDJ|1|1H|G|497
5NDJ|1|1H|A|498
5NDJ|1|1H|A|499
5NDJ|1|1H|A|500
5NDJ|1|1H|G|501

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 31

50S ribosomal protein L4

Chain C8

50S ribosomal protein L20

Chain F8

50S ribosomal protein L23

Chain P8

50S ribosomal protein L34