IL_5NDW_404

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

AG*CAUU

Length

6 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_5NDW_404 not in the Motif Atlas

Homologous match to IL_4V88_428

Geometric discrepancy: 0.0898

The information below is about IL_4V88_428

Detailed Annotation

Major groove platform; stack outside cWW

Broad Annotation

No text annotation

Motif group

IL_50694.4

Basepair signature

cWW-cWW-tSH-cWW-R

Number of instances in this motif group

28

Unit IDs

5NDW|1|6|A|865
5NDW|1|6|G|866
*
5NDW|1|6|C|962
5NDW|1|6|A|963
5NDW|1|6|U|964
5NDW|1|6|U|965

Current chains

Chain 6

18S ribosomal RNA

Nearby chains

Chain c3

40S ribosomal protein S13

Chain d2

40S ribosomal protein S22-A

Chain d7

40S ribosomal protein S27-A