J3_5NDJ_060

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*CGCCAGAGAG*CGUAG

Length

20 nucleotides

Bulged bases

5NDJ|1|14|G|346

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_060 not in the Motif Atlas

Homologous match to J3_9DFE_006

Geometric discrepancy: 0.0624

The information below is about J3_9DFE_006

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_46299.2

Basepair signature

cWW-F-F-F-cHH-cWW-tHS-F-cWW-cSW-tHS-cWW

Number of instances in this motif group

3

Unit IDs

5NDJ|1|14|C|322
5NDJ|1|14|G|323
5NDJ|1|14|A|324
5NDJ|1|14|A|325
5NDJ|1|14|G|326
*
5NDJ|1|14|C|341
5NDJ|1|14|G|342
5NDJ|1|14|C|343
5NDJ|1|14|C|344
5NDJ|1|14|A|345
5NDJ|1|14|G|346
5NDJ|1|14|A|347
5NDJ|1|14|G|348
5NDJ|1|14|A|349
5NDJ|1|14|G|350
*
5NDJ|1|14|C|362
5NDJ|1|14|G|363
5NDJ|1|14|U|364
5NDJ|1|14|A|365
5NDJ|1|14|G|366

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 39

50S ribosomal protein L4

Chain C5

50S ribosomal protein L24