J4_5NDJ_026

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

CAAAG*CUGAC*GGG*CGG

Length

16 nucleotides

Bulged bases

5NDJ|1|1H|A|2303, 5NDJ|1|1H|G|2397

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_026 not in the Motif Atlas

Homologous match to J4_4WF9_008

Geometric discrepancy: 0.1565

The information below is about J4_4WF9_008

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_98139.1

Basepair signature

cWW-F-cWW-tWW-tHH-cWW-cHW-cWW

Number of instances in this motif group

6

Unit IDs

5NDJ|1|1H|C|2300
5NDJ|1|1H|A|2301
5NDJ|1|1H|A|2302
5NDJ|1|1H|A|2303
5NDJ|1|1H|G|2304
*
5NDJ|1|1H|C|2358
5NDJ|1|1H|U|2359
5NDJ|1|1H|G|2360
5NDJ|1|1H|A|2361
5NDJ|1|1H|C|2362
*
5NDJ|1|1H|G|2385
5NDJ|1|1H|G|2386
5NDJ|1|1H|G|2387
*
5NDJ|1|1H|C|2396
5NDJ|1|1H|G|2397
5NDJ|1|1H|G|2398

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain A8

50S ribosomal protein L18

Chain I8

50S ribosomal protein L27

Chain Q8

50S ribosomal protein L35