J3_5NDJ_023

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

CUC*GAG*UAGAAG

Length

12 nucleotides

Bulged bases

5NDJ|1|14|G|2349

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

J3_5NDJ_023 not in the Motif Atlas

Homologous match to J3_7RQB_011

Geometric discrepancy: 0.0689

The information below is about J3_7RQB_011

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_91491.4

Basepair signature

cWW-F-tWW-tHW-cWW-F-cWW

Number of instances in this motif group

7

Unit IDs

5NDJ|1|14|C|2310
5NDJ|1|14|U|2311
5NDJ|1|14|C|2312
*
5NDJ|1|14|G|2336
5NDJ|1|14|A|2337
5NDJ|1|14|G|2338
*
5NDJ|1|14|U|2347
5NDJ|1|14|A|2348
5NDJ|1|14|G|2349
5NDJ|1|14|A|2350
5NDJ|1|14|A|2351
5NDJ|1|14|G|2352

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

Chain X4

Transfer RNA; tRNA