IL_5NDJ_292

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

GGAA*UC

Length

6 nucleotides

Bulged bases

None detected

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

IL_5NDJ_292 not in the Motif Atlas

Geometric match to IL_7RQB_066

Geometric discrepancy: 0.0688

The information below is about IL_7RQB_066

Detailed Annotation

Major groove platform; stack outside cWW

Broad Annotation

Major groove platform

Motif group

IL_50694.2

Basepair signature

cWW-tSH-cWW-L

Number of instances in this motif group

27

Unit IDs

5NDJ|1|1H|G|1716
5NDJ|1|1H|G|1717
5NDJ|1|1H|A|1718
5NDJ|1|1H|A|1719
*
5NDJ|1|1H|U|2018
5NDJ|1|1H|C|2019

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 21

50S ribosomal protein L3

Chain 68

50S ribosomal protein L14