J3_5NDK_016

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

CGAGCUA*UAG*CGAG

Length

14 nucleotides

Bulged bases

5NDK|1|14|G|735, 5NDK|1|14|G|841

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_016 not in the Motif Atlas

Homologous match to J3_7A0S_004

Geometric discrepancy: 0.0928

The information below is about J3_7A0S_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_46658.1

Basepair signature

cWW-tWH-cWW-tSW-F-F-cWW

Number of instances in this motif group

10

Unit IDs

5NDK|1|14|C|732
5NDK|1|14|G|733
5NDK|1|14|A|734
5NDK|1|14|G|735
5NDK|1|14|C|736
5NDK|1|14|U|737
5NDK|1|14|A|738
*
5NDK|1|14|U|822
5NDK|1|14|A|823
5NDK|1|14|G|824
*
5NDK|1|14|C|840
5NDK|1|14|G|841
5NDK|1|14|A|842
5NDK|1|14|G|843

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 19

50S ribosomal protein L2

Chain L5

50S ribosomal protein L34