J3_5NDW_023

3D structure

PDB id

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

Description

Crystal structure of aminoglycoside TC007 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

5NDW|1|2|A|1217, 5NDW|1|2|G|1445

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_5NDW_023 not in the Motif Atlas

Homologous match to J3_4V88_038

Geometric discrepancy: 0.088

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

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