J3_5NDW_069

3D structure

PDB id

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

Description

Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

3.7 Å

Loop

Sequence

AGAUUAAG*CGCGCAAAU*AGU

Length

20 nucleotides

Bulged bases

5NDW|1|2|A|47

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_5NDW_069 not in the Motif Atlas

Homologous match to J3_8P9A_069

Geometric discrepancy: 0.064

The information below is about J3_8P9A_069

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_63856.1

Basepair signature

cWW-cWW-cSW-F-cWW-F-tHH-F-cWW-F-F-F-F

Number of instances in this motif group

5

Unit IDs

5NDW|1|2|A|41
5NDW|1|2|G|42
5NDW|1|2|A|43
5NDW|1|2|U|44
5NDW|1|2|U|45
5NDW|1|2|A|46
5NDW|1|2|A|47
5NDW|1|2|G|48
*
5NDW|1|2|C|431
5NDW|1|2|G|432
5NDW|1|2|C|433
5NDW|1|2|G|434
5NDW|1|2|C|435
5NDW|1|2|A|436
5NDW|1|2|A|437
5NDW|1|2|A|438
5NDW|1|2|U|439
*
5NDW|1|2|A|464
5NDW|1|2|G|465
5NDW|1|2|U|466

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain D3

40S ribosomal protein S23-A

Chain S9

40S ribosomal protein S9-A