J3_5NDJ_025

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

CC*GUGGAU*AAUCG

Length

13 nucleotides

Bulged bases

5NDJ|1|14|G|2846

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_025 not in the Motif Atlas

Homologous match to J3_9DFE_019

Geometric discrepancy: 0.1102

The information below is about J3_9DFE_019

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_76911.2

Basepair signature

cWW-tHS-F-F-F-cWW-cWW

Number of instances in this motif group

4

Unit IDs

5NDJ|1|14|C|2827
5NDJ|1|14|C|2828
*
5NDJ|1|14|G|2844
5NDJ|1|14|U|2845
5NDJ|1|14|G|2846
5NDJ|1|14|G|2847
5NDJ|1|14|A|2848
5NDJ|1|14|U|2849
*
5NDJ|1|14|A|2895
5NDJ|1|14|A|2896
5NDJ|1|14|U|2897
5NDJ|1|14|C|2898
5NDJ|1|14|G|2899

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 29

50S ribosomal protein L3

Chain 55

50S ribosomal protein L17

Chain J5

50S ribosomal protein L32