HL_5NDJ_146

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

GUGAAAGCC

Length

9 nucleotides

Bulged bases

5NDJ|1|1H|G|354

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

HL_5NDJ_146 not in the Motif Atlas

Homologous match to HL_7RQB_012

Geometric discrepancy: 0.0783

The information below is about HL_7RQB_012

Detailed Annotation

T-loop with unstacked turn

Broad Annotation

T-loop

Motif group

HL_08002.9

Basepair signature

cWW-tWH-F-F

Number of instances in this motif group

19

Unit IDs

5NDJ|1|1H|G|352
5NDJ|1|1H|U|353
5NDJ|1|1H|G|354
5NDJ|1|1H|A|355
5NDJ|1|1H|A|356
5NDJ|1|1H|A|357
5NDJ|1|1H|G|358
5NDJ|1|1H|C|359
5NDJ|1|1H|C|360

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 31

50S ribosomal protein L4

Chain G8

50S ribosomal protein L24