IL_5NDJ_020

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

CGGCCAAC*GG

Length

10 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_020 not in the Motif Atlas

Homologous match to IL_5J7L_024

Geometric discrepancy: 0.0748

The information below is about IL_5J7L_024

Detailed Annotation

SSU/LSU pseudoknot

Broad Annotation

No text annotation

Motif group

IL_41203.4

Basepair signature

cWW-L-cWW-L-L-R-cSH

Number of instances in this motif group

11

Unit IDs

5NDJ|1|13|C|1133
5NDJ|1|13|G|1134
5NDJ|1|13|G|1135
5NDJ|1|13|C|1136
5NDJ|1|13|C|1137
5NDJ|1|13|A|1138
5NDJ|1|13|A|1139
5NDJ|1|13|C|1140
*
5NDJ|1|13|G|1169
5NDJ|1|13|G|1170

Current chains

Chain 13

16S ribosomal RNA

Nearby chains

Chain 3E

30S ribosomal protein S4

Chain 3I

30S ribosomal protein S12