IL_5NDW_218

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

AGGAU*AGAAU

Length

10 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_218 not in the Motif Atlas

Homologous match to IL_4V88_474

Geometric discrepancy: 0.1103

The information below is about IL_4V88_474

Detailed Annotation

Triple sheared

Broad Annotation

No text annotation

Motif group

IL_95716.2

Basepair signature

cWW-cWW-tHS-tHS-tSH-cWW

Number of instances in this motif group

18

Unit IDs

5NDW|1|2|A|1678
5NDW|1|2|G|1679
5NDW|1|2|G|1680
5NDW|1|2|A|1681
5NDW|1|2|U|1682
*
5NDW|1|2|A|1719
5NDW|1|2|G|1720
5NDW|1|2|A|1721
5NDW|1|2|A|1722
5NDW|1|2|U|1723

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain N4

60S ribosomal protein L24-A

Chain S6

40S ribosomal protein S6-A

Chain S8

40S ribosomal protein S8-A