J3_5NDK_045

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

CGUAAG*CGG*UCAG

Length

13 nucleotides

Bulged bases

5NDK|1|1H|A|1351

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_045 not in the Motif Atlas

Homologous match to J3_7RQB_007

Geometric discrepancy: 0.0611

The information below is about J3_7RQB_007

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_32852.3

Basepair signature

cWW-tSH-tHW-F-F-cWW-cWW-F

Number of instances in this motif group

4

Unit IDs

5NDK|1|1H|C|1347
5NDK|1|1H|G|1348
5NDK|1|1H|U|1349
5NDK|1|1H|A|1350
5NDK|1|1H|A|1351
5NDK|1|1H|G|1352
*
5NDK|1|1H|C|1674
5NDK|1|1H|G|1675
5NDK|1|1H|G|1676
*
5NDK|1|1H|U|1689
5NDK|1|1H|C|1690
5NDK|1|1H|A|1691
5NDK|1|1H|G|1692

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains