IL_5NDJ_320

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

CCGAG*CGGCG

Length

10 nucleotides

Bulged bases

None detected

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

IL_5NDJ_320 not in the Motif Atlas

Homologous match to IL_5J7L_338

Geometric discrepancy: 0.1726

The information below is about IL_5J7L_338

Detailed Annotation

Double sheared with non-canonical cWW

Broad Annotation

Double sheared

Motif group

IL_17948.2

Basepair signature

cWW-L-R-tSH-tHS-cWW

Number of instances in this motif group

13

Unit IDs

5NDJ|1|1H|C|2481
5NDJ|1|1H|C|2482
5NDJ|1|1H|G|2483
5NDJ|1|1H|A|2484
5NDJ|1|1H|G|2485
*
5NDJ|1|1H|C|2495
5NDJ|1|1H|G|2496
5NDJ|1|1H|G|2497
5NDJ|1|1H|C|2498
5NDJ|1|1H|G|2499

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 88

50S ribosomal protein L16

Chain W1

Transfer RNA; tRNA