J5_5NDJ_008

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

AAAAGACC*GGAUAACA*UCGAUGUC*GGUUCAG*CGGUCU

Length

37 nucleotides

Bulged bases

5NDJ|1|14|A|2087, 5NDJ|1|14|A|2463, 5NDJ|1|14|U|2464, 5NDJ|1|14|U|2624

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|A|2082
5NDJ|1|14|A|2083
5NDJ|1|14|A|2084
5NDJ|1|14|A|2085
5NDJ|1|14|G|2086
5NDJ|1|14|A|2087
5NDJ|1|14|C|2088
5NDJ|1|14|C|2089
*
5NDJ|1|14|G|2461
5NDJ|1|14|G|2462
5NDJ|1|14|A|2463
5NDJ|1|14|U|2464
5NDJ|1|14|A|2465
5NDJ|1|14|A|2466
5NDJ|1|14|C|2467
5NDJ|1|14|A|2468
*
5NDJ|1|14|U|2515
5NDJ|1|14|C|2516
5NDJ|1|14|G|2517
5NDJ|1|14|A|2518
5NDJ|1|14|U|2519
5NDJ|1|14|G|2520
5NDJ|1|14|U|2521
5NDJ|1|14|C|2522
*
5NDJ|1|14|G|2597
5NDJ|1|14|G|2598
5NDJ|1|14|U|2599
5NDJ|1|14|U|2600
5NDJ|1|14|C|2601
5NDJ|1|14|A|2602
5NDJ|1|14|G|2603
*
5NDJ|1|14|C|2621
5NDJ|1|14|G|2622
5NDJ|1|14|G|2623
5NDJ|1|14|U|2624
5NDJ|1|14|C|2625
5NDJ|1|14|U|2626

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 19

50S ribosomal protein L2

Chain 29

50S ribosomal protein L3

Chain 35

50S ribosomal protein L15

Chain 39

50S ribosomal protein L4

Chain 45

50S ribosomal protein L16

Chain A5

50S ribosomal protein L22

Chain E5

50S ribosomal protein L27

Chain J5

50S ribosomal protein L32

Chain W4

Transfer RNA; tRNA

Chain X4

Transfer RNA; tRNA