IL_5NDK_325

3D structure

PDB id

5NDK (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA

Experimental method

X-RAY DIFFRACTION

Resolution

2.95 Å

Loop

Sequence

CUC*GCGAG

Length

8 nucleotides

Bulged bases

5NDK|1|1H|G|2591, 5NDK|1|1H|A|2592

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_5NDK_325 not in the Motif Atlas

Homologous match to IL_7RQB_097

Geometric discrepancy: 0.0558

The information below is about IL_7RQB_097

Detailed Annotation

Isolated non-canonical cWW with bulges

Broad Annotation

Isolated non-canonical cWW with bulges

Motif group

IL_90933.2

Basepair signature

cWW-cWW-cWW

Number of instances in this motif group

11

Unit IDs

5NDK|1|1H|C|2525
5NDK|1|1H|U|2526
5NDK|1|1H|C|2527
*
5NDK|1|1H|G|2589
5NDK|1|1H|C|2590
5NDK|1|1H|G|2591
5NDK|1|1H|A|2592
5NDK|1|1H|G|2593

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 21

50S ribosomal protein L3

Chain N8

50S ribosomal protein L32