J3_5NDG_025

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

UG*UGUC*GAUAA

Length

11 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_025 not in the Motif Atlas

Homologous match to J3_8C3A_085

Geometric discrepancy: 0.0961

The information below is about J3_8C3A_085

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_76043.2

Basepair signature

cWW-F-F-F-F-tSS-cWW-cWW

Number of instances in this motif group

3

Unit IDs

5NDG|1|2|U|1293
5NDG|1|2|G|1294
*
5NDG|1|2|U|1303
5NDG|1|2|G|1304
5NDG|1|2|U|1305
5NDG|1|2|C|1306
*
5NDG|1|2|G|1318
5NDG|1|2|A|1319
5NDG|1|2|U|1320
5NDG|1|2|A|1321
5NDG|1|2|A|1322

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain C7

40S ribosomal protein S17-A

Chain S0

40S ribosomal protein S0-A

Chain S2

40S ribosomal protein S2