J3_5NDK_042

3D structure

PDB id

5NDK (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA

Experimental method

X-RAY DIFFRACTION

Resolution

2.95 Å

Loop

Sequence

UAAAC*GGGUCGUG*CG

Length

15 nucleotides

Bulged bases

5NDK|1|1H|U|289

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_5NDK_042 not in the Motif Atlas

Homologous match to J3_7RQB_003

Geometric discrepancy: 0.0636

The information below is about J3_7RQB_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_97921.1

Basepair signature

cWW-F-F-tSH-tWH-F-cWW-F-cWW

Number of instances in this motif group

2

Unit IDs

5NDK|1|1H|U|259
5NDK|1|1H|A|260
5NDK|1|1H|A|261
5NDK|1|1H|A|262
5NDK|1|1H|C|263
*
5NDK|1|1H|G|283
5NDK|1|1H|G|284
5NDK|1|1H|G|285
5NDK|1|1H|U|286
5NDK|1|1H|C|287
5NDK|1|1H|G|288
5NDK|1|1H|U|289
5NDK|1|1H|G|290
*
5NDK|1|1H|C|397
5NDK|1|1H|G|398

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 61

50S ribosomal protein L9