IL_5NDG_151

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

UAUCAA*UUUCAACG

Length

14 nucleotides

Bulged bases

5NDG|1|2|U|313, 5NDG|1|2|C|351

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

IL_5NDG_151 not in the Motif Atlas

Homologous match to IL_4V88_402

Geometric discrepancy: 0.0895

The information below is about IL_4V88_402

Detailed Annotation

Kink-turn with non-sequential stacking

Broad Annotation

Kink-turn

Motif group

IL_45067.5

Basepair signature

cWW-tSH-tSS-tHS-R-cWW-cWW-R

Number of instances in this motif group

16

Unit IDs

5NDG|1|2|U|311
5NDG|1|2|A|312
5NDG|1|2|U|313
5NDG|1|2|C|314
5NDG|1|2|A|315
5NDG|1|2|A|316
*
5NDG|1|2|U|348
5NDG|1|2|U|349
5NDG|1|2|U|350
5NDG|1|2|C|351
5NDG|1|2|A|352
5NDG|1|2|A|353
5NDG|1|2|C|354
5NDG|1|2|G|355

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain C1

40S ribosomal protein S11-A

Chain D3

40S ribosomal protein S23-A

Chain S8

40S ribosomal protein S8-A