J3_5NDK_020

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

CAAG*CGCAAAC*GUG

Length

14 nucleotides

Bulged bases

5NDK|1|14|A|1658

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_020 not in the Motif Atlas

Homologous match to J3_7RQB_008

Geometric discrepancy: 0.0527

The information below is about J3_7RQB_008

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_16623.1

Basepair signature

cWW-tSH-tWW-tHH-F-tHW-cWW-F-cWW

Number of instances in this motif group

2

Unit IDs

5NDK|1|14|C|1355
5NDK|1|14|A|1356
5NDK|1|14|A|1357
5NDK|1|14|G|1358
*
5NDK|1|14|C|1654
5NDK|1|14|G|1655
5NDK|1|14|C|1656
5NDK|1|14|A|1657
5NDK|1|14|A|1658
5NDK|1|14|A|1659
5NDK|1|14|C|1660
*
5NDK|1|14|G|1669
5NDK|1|14|U|1670
5NDK|1|14|G|1671

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain L5

50S ribosomal protein L34