J4_5NDJ_020

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

CGAUAAA*UC*GCGC*GG

Length

15 nucleotides

Bulged bases

5NDJ|1|1H|G|1320, 5NDJ|1|1H|A|1321, 5NDJ|1|1H|U|1322, 5NDJ|1|1H|G|1697

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_020 not in the Motif Atlas

Homologous match to J4_9DFE_003

Geometric discrepancy: 0.0602

The information below is about J4_9DFE_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_64571.5

Basepair signature

cWW-F-cWW-tSS-cWW-F-cWW

Number of instances in this motif group

4

Unit IDs

5NDJ|1|1H|C|1319
5NDJ|1|1H|G|1320
5NDJ|1|1H|A|1321
5NDJ|1|1H|U|1322
5NDJ|1|1H|A|1323
5NDJ|1|1H|A|1324
5NDJ|1|1H|A|1325
*
5NDJ|1|1H|U|1343
5NDJ|1|1H|C|1344
*
5NDJ|1|1H|G|1695
5NDJ|1|1H|C|1696
5NDJ|1|1H|G|1697
5NDJ|1|1H|C|1698
*
5NDJ|1|1H|G|2034
5NDJ|1|1H|G|2035

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 98

50S ribosomal protein L17

Chain E8

50S ribosomal protein L22

Chain N8

50S ribosomal protein L32