IL_5NDW_161

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

GUC*GC

Length

5 nucleotides

Bulged bases

5NDW|1|2|U|558

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_5NDW_161 not in the Motif Atlas

Geometric match to IL_4V88_414

Geometric discrepancy: 0.1969

The information below is about IL_4V88_414

Detailed Annotation

Single bulged U

Broad Annotation

No text annotation

Motif group

IL_83039.19

Basepair signature

cWW-L-cWW

Number of instances in this motif group

123

Unit IDs

5NDW|1|2|G|557
5NDW|1|2|U|558
5NDW|1|2|C|559
*
5NDW|1|2|G|586
5NDW|1|2|C|587

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain E0

40S ribosomal protein S30-A

Chain S3

40S ribosomal protein S3

Chain SM

Suppressor protein STM1