J4_5NDJ_018

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

CU*GAGUAC*GGAAUCUG*UAAG

Length

20 nucleotides

Bulged bases

5NDJ|1|1H|U|433

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_018 not in the Motif Atlas

Homologous match to J4_9DFE_001

Geometric discrepancy: 0.1395

The information below is about J4_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_45801.6

Basepair signature

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

Number of instances in this motif group

7

Unit IDs

5NDJ|1|1H|C|258
5NDJ|1|1H|U|259
*
5NDJ|1|1H|G|398
5NDJ|1|1H|A|399
5NDJ|1|1H|G|400
5NDJ|1|1H|U|401
5NDJ|1|1H|A|402
5NDJ|1|1H|C|403
*
5NDJ|1|1H|G|427
5NDJ|1|1H|G|428
5NDJ|1|1H|A|429
5NDJ|1|1H|A|430
5NDJ|1|1H|U|431
5NDJ|1|1H|C|432
5NDJ|1|1H|U|433
5NDJ|1|1H|G|434
*
5NDJ|1|1H|U|450
5NDJ|1|1H|A|451
5NDJ|1|1H|A|452
5NDJ|1|1H|G|453

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 61

50S ribosomal protein L9

Chain J8

50S ribosomal protein L28