J3_5NDJ_058

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

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

5NDJ|1|14|U|531, 5NDJ|1|14|G|535

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_058 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.056

The information below is about J3_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_92134.2

Basepair signature

cWW-cWW-cWW-F-tWH-cSS-tSS-tSH-tSH-tWW-tHH-tWH-tWW-F-F-cSS-cSW-F-tHS-cWW

Number of instances in this motif group

6

Unit IDs

5NDJ|1|14|G|30
5NDJ|1|14|C|31
*
5NDJ|1|14|G|502
5NDJ|1|14|U|503
5NDJ|1|14|G|504
5NDJ|1|14|A|505
5NDJ|1|14|A|506
5NDJ|1|14|A|507
5NDJ|1|14|A|508
5NDJ|1|14|G|509
5NDJ|1|14|A|510
5NDJ|1|14|A|511
5NDJ|1|14|C|512
*
5NDJ|1|14|G|523
5NDJ|1|14|A|524
5NDJ|1|14|G|525
5NDJ|1|14|U|526
5NDJ|1|14|G|527
5NDJ|1|14|A|528
5NDJ|1|14|A|529
5NDJ|1|14|A|530
5NDJ|1|14|U|531
5NDJ|1|14|A|532
5NDJ|1|14|G|533
5NDJ|1|14|A|534
5NDJ|1|14|G|535
5NDJ|1|14|C|536
5NDJ|1|14|C|537

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 85

50S ribosomal protein L20

Chain A5

50S ribosomal protein L22

Chain C5

50S ribosomal protein L24