IL_5NDG_135

3D structure

PDB id

5NDG (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of geneticin (G418) bound to the yeast 80S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

3.7 Å

Loop

Sequence

UCAAA*UGACAA

Length

11 nucleotides

Bulged bases

5NDG|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_5NDG_135 not in the Motif Atlas

Homologous match to IL_4V88_386

Geometric discrepancy: 0.0823

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

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