J6_5NDJ_002

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

UUUA*UUUG*CG*CGCC*GCCUAGUGAACC*GAUCAACGGAUAAAA

Length

41 nucleotides

Bulged bases

5NDJ|1|14|U|2101, 5NDJ|1|14|A|2403, 5NDJ|1|14|U|2405, 5NDJ|1|14|G|2443, 5NDJ|1|14|A|2445, 5NDJ|1|14|U|2446

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

5NDJ|1|14|U|2099
5NDJ|1|14|U|2100
5NDJ|1|14|U|2101
5NDJ|1|14|A|2102
*
5NDJ|1|14|U|2258
5NDJ|1|14|U|2259
5NDJ|1|14|U|2260
5NDJ|1|14|G|2261
*
5NDJ|1|14|C|2273
5NDJ|1|14|G|2274
*
5NDJ|1|14|C|2296
5NDJ|1|14|G|2297
5NDJ|1|14|C|2298
5NDJ|1|14|C|2299
*
5NDJ|1|14|G|2399
5NDJ|1|14|C|2400
5NDJ|1|14|C|2401
5NDJ|1|14|U|2402
5NDJ|1|14|A|2403
5NDJ|1|14|G|2404
5NDJ|1|14|U|2405
5NDJ|1|14|G|2406
5NDJ|1|14|A|2407
5NDJ|1|14|A|2408
5NDJ|1|14|C|2409
5NDJ|1|14|C|2410
*
5NDJ|1|14|G|2436
5NDJ|1|14|A|2437
5NDJ|1|14|U|2438
5NDJ|1|14|C|2439
5NDJ|1|14|A|2440
5NDJ|1|14|A|2441
5NDJ|1|14|C|2442
5NDJ|1|14|G|2443
5NDJ|1|14|G|2444
5NDJ|1|14|A|2445
5NDJ|1|14|U|2446
5NDJ|1|14|A|2447
5NDJ|1|14|A|2448
5NDJ|1|14|A|2449
5NDJ|1|14|A|2450

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 19

50S ribosomal protein L2

Chain 35

50S ribosomal protein L15

Chain E5

50S ribosomal protein L27

Chain F5

50S ribosomal protein L28

Chain M5

50S ribosomal protein L35

Chain V4

Transfer RNA; tRNA