IL_5NDJ_097

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

CCCCCAAG*CG

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_097 not in the Motif Atlas

Geometric match to IL_5J7L_278

Geometric discrepancy: 0.1128

The information below is about IL_5J7L_278

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|14|C|1052
5NDJ|1|14|C|1053
5NDJ|1|14|C|1054
5NDJ|1|14|C|1055
5NDJ|1|14|C|1056
5NDJ|1|14|A|1057
5NDJ|1|14|A|1058
5NDJ|1|14|G|1059
*
5NDJ|1|14|C|1199
5NDJ|1|14|G|1200

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 15

50S ribosomal protein L13

Chain 85

50S ribosomal protein L20