IL_5NDW_488

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

GUA*UUUUC

Length

8 nucleotides

Bulged bases

5NDW|1|2|U|260

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_488 not in the Motif Atlas

Homologous match to IL_8P9A_386

Geometric discrepancy: 0.2349

The information below is about IL_8P9A_386

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_36931.2

Basepair signature

cWW-cSH-cWW-cWW

Number of instances in this motif group

24

Unit IDs

5NDW|1|2|G|204
5NDW|1|2|U|205
5NDW|1|2|A|206
*
5NDW|1|2|U|259
5NDW|1|2|U|260
5NDW|1|2|U|261
5NDW|1|2|U|262
5NDW|1|2|C|263

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain S4

40S ribosomal protein S4-A

Chain S6

40S ribosomal protein S6-A

Chain S8

40S ribosomal protein S8-A