J4_5NDJ_009

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

UC*GGUUAG*CU*ACCCGUA

Length

17 nucleotides

Bulged bases

5NDJ|1|14|U|1390

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

J4_5NDJ_009 not in the Motif Atlas

Homologous match to J4_9DFE_005

Geometric discrepancy: 0.1018

The information below is about J4_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_10313.5

Basepair signature

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

Number of instances in this motif group

5

Unit IDs

5NDJ|1|14|U|1362
5NDJ|1|14|C|1363
*
5NDJ|1|14|G|1387
5NDJ|1|14|G|1388
5NDJ|1|14|U|1389
5NDJ|1|14|U|1390
5NDJ|1|14|A|1391
5NDJ|1|14|G|1392
*
5NDJ|1|14|C|1453
5NDJ|1|14|U|1454
*
5NDJ|1|14|A|1646
5NDJ|1|14|C|1647
5NDJ|1|14|C|1648
5NDJ|1|14|C|1649
5NDJ|1|14|G|1650
5NDJ|1|14|U|1651
5NDJ|1|14|A|1652

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain B5

50S ribosomal protein L23