IL_5NDJ_228

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

CGAAG*CGAG

Length

9 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_228 not in the Motif Atlas

Geometric match to IL_4LFB_062

Geometric discrepancy: 0.0884

The information below is about IL_4LFB_062

Detailed Annotation

UAA/GAN variation

Broad Annotation

UAA/GAN variation

Motif group

IL_77691.5

Basepair signature

cWW-tSH-L-R-L-cWW

Number of instances in this motif group

7

Unit IDs

5NDJ|1|1G|C|2059
5NDJ|1|1G|G|2060
5NDJ|1|1G|A|2061
5NDJ|1|1G|A|2062
5NDJ|1|1G|G|2063
*
5NDJ|1|1G|C|2089
5NDJ|1|1G|G|2090
5NDJ|1|1G|A|2091
5NDJ|1|1G|G|2092

Current chains

Chain 1G

16S ribosomal RNA

Nearby chains

Chain 14

Large subunit ribosomal RNA; LSU rRNA

Chain 75

50S ribosomal protein L19

Chain BA

30S ribosomal protein S20