J3_5NDG_015

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

AG*CGCAAAU*AGU

Length

12 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

J3_5NDG_015 not in the Motif Atlas

Homologous match to J3_8P9A_068

Geometric discrepancy: 0.0814

The information below is about J3_8P9A_068

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_67856.4

Basepair signature

cWW-cWW-cSW-cWW-F-F-F-F

Number of instances in this motif group

4

Unit IDs

5NDG|1|2|A|41
5NDG|1|2|G|42
*
5NDG|1|2|C|433
5NDG|1|2|G|434
5NDG|1|2|C|435
5NDG|1|2|A|436
5NDG|1|2|A|437
5NDG|1|2|A|438
5NDG|1|2|U|439
*
5NDG|1|2|A|464
5NDG|1|2|G|465
5NDG|1|2|U|466

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain D3

40S ribosomal protein S23-A

Chain S9

40S ribosomal protein S9-A