IL_5NDJ_093

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

GGG*CUAC

Length

7 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_093 not in the Motif Atlas

Geometric match to IL_3LOA_003

Geometric discrepancy: 0.3769

The information below is about IL_3LOA_003

Detailed Annotation

Decoding loop with one bulged A

Broad Annotation

Decoding loop with one bulged A

Motif group

IL_08770.1

Basepair signature

cWW-L-R-cWW

Number of instances in this motif group

5

Unit IDs

5NDJ|1|14|G|929
5NDJ|1|14|G|930
5NDJ|1|14|G|931
*
5NDJ|1|14|C|942
5NDJ|1|14|U|943
5NDJ|1|14|A|944
5NDJ|1|14|C|945

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 45

50S ribosomal protein L16

Chain W4

Transfer RNA; tRNA