J3_5NDG_023

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

CCAGAC*GGGUG*UUAGACG

Length

18 nucleotides

Bulged bases

5NDG|1|2|A|1217, 5NDG|1|2|G|1445, 5NDG|1|2|C|1447

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_023 not in the Motif Atlas

Homologous match to J3_4V88_038

Geometric discrepancy: 0.0995

The information below is about J3_4V88_038

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_75993.1

Basepair signature

cWW-tWH-F-F-tHS-cWW-cWW-cWW-F

Number of instances in this motif group

2

Unit IDs

5NDG|1|2|C|1215
5NDG|1|2|C|1216
5NDG|1|2|A|1217
5NDG|1|2|G|1218
5NDG|1|2|A|1219
5NDG|1|2|C|1220
*
5NDG|1|2|G|1263
5NDG|1|2|G|1264
5NDG|1|2|G|1265
5NDG|1|2|U|1266
5NDG|1|2|G|1267
*
5NDG|1|2|U|1442
5NDG|1|2|U|1443
5NDG|1|2|A|1444
5NDG|1|2|G|1445
5NDG|1|2|A|1446
5NDG|1|2|C|1447
5NDG|1|2|G|1448

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain C0

40S ribosomal protein S10-A

Chain D9

40S ribosomal protein S29-A

Chain E1

Ubiquitin-40S ribosomal protein S31