J4_5NDG_018

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

GG*CU*AG*UC

Length

8 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

J4_5NDG_018 not in the Motif Atlas

Homologous match to J4_8P9A_016

Geometric discrepancy: 0.0896

The information below is about J4_8P9A_016

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_24280.2

Basepair signature

cWW-cWW-cWW-cWW

Number of instances in this motif group

5

Unit IDs

5NDG|1|5|G|1674
5NDG|1|5|G|1675
*
5NDG|1|5|C|1693
5NDG|1|5|U|1694
*
5NDG|1|5|A|1752
5NDG|1|5|G|1753
*
5NDG|1|5|U|1772
5NDG|1|5|C|1773

Current chains

Chain 5

25S ribosomal RNA

Nearby chains

Chain n2

60S ribosomal protein L22-A

Chain o4

60S ribosomal protein L34-A

Chain o8

60S ribosomal protein L38