J3_5NDJ_050

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

CAUC*GUU*AUUAAAG

Length

14 nucleotides

Bulged bases

5NDJ|1|1H|A|2533, 5NDJ|1|1H|U|2534

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_050 not in the Motif Atlas

Homologous match to J3_7RQB_012

Geometric discrepancy: 0.055

The information below is about J3_7RQB_012

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_32601.3

Basepair signature

cWW-tWH-cHW-tSH-cWW-tSS-F-cSS-cWW

Number of instances in this motif group

4

Unit IDs

5NDJ|1|1H|C|2532
5NDJ|1|1H|A|2533
5NDJ|1|1H|U|2534
5NDJ|1|1H|C|2535
*
5NDJ|1|1H|G|2560
5NDJ|1|1H|U|2561
5NDJ|1|1H|U|2562
*
5NDJ|1|1H|A|2576
5NDJ|1|1H|U|2577
5NDJ|1|1H|U|2578
5NDJ|1|1H|A|2579
5NDJ|1|1H|A|2580
5NDJ|1|1H|A|2581
5NDJ|1|1H|G|2582

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 58

50S ribosomal protein L13

Chain 68

50S ribosomal protein L14