IL_5NDW_135

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

UCAAA*UGACAA

Length

11 nucleotides

Bulged bases

5NDW|1|2|A|468

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_135 not in the Motif Atlas

Geometric match to IL_4V88_386

Geometric discrepancy: 0.1042

The information below is about IL_4V88_386

Detailed Annotation

Triple sheared related

Broad Annotation

Triple sheared

Motif group

IL_37842.2

Basepair signature

cWW-cWW-L-R-cWW-cWW-R-L

Number of instances in this motif group

4

Unit IDs

5NDW|1|2|U|37
5NDW|1|2|C|38
5NDW|1|2|A|39
5NDW|1|2|A|40
5NDW|1|2|A|41
*
5NDW|1|2|U|466
5NDW|1|2|G|467
5NDW|1|2|A|468
5NDW|1|2|C|469
5NDW|1|2|A|470
5NDW|1|2|A|471

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain D4

40S ribosomal protein S24-A

Chain S4

40S ribosomal protein S4-A

Chain S9

40S ribosomal protein S9-A