IL_5NDJ_146

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

CAG*CGGAG

Length

8 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_146 not in the Motif Atlas

Geometric match to IL_4WF9_086

Geometric discrepancy: 0.3414

The information below is about IL_4WF9_086

Detailed Annotation

Isolated tHS basepair with bulges

Broad Annotation

No text annotation

Motif group

IL_61476.2

Basepair signature

cWW-tSH-L-cWW-L

Number of instances in this motif group

7

Unit IDs

5NDJ|1|14|C|2312
5NDJ|1|14|A|2313
5NDJ|1|14|G|2314
*
5NDJ|1|14|C|2332
5NDJ|1|14|G|2333
5NDJ|1|14|G|2334
5NDJ|1|14|A|2335
5NDJ|1|14|G|2336

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 1J

5S ribosomal RNA; 5S rRNA

Chain 49

50S ribosomal protein L5

Chain 65

50S ribosomal protein L18

Chain E5

50S ribosomal protein L27