J6_5NDG_001

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

GAGUAC*GGAAAAGAAAC*GGAUU*AAAAG*CUAAAUAUUGG*CAUC

Length

42 nucleotides

Bulged bases

5NDG|1|1|A|67, 5NDG|1|1|U|329, 5NDG|1|4|U|34

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

5NDG|1|1|G|22
5NDG|1|1|A|23
5NDG|1|1|G|24
5NDG|1|1|U|25
5NDG|1|1|A|26
5NDG|1|1|C|27
*
5NDG|1|1|G|58
5NDG|1|1|G|59
5NDG|1|1|A|60
5NDG|1|1|A|61
5NDG|1|1|A|62
5NDG|1|1|A|63
5NDG|1|1|G|64
5NDG|1|1|A|65
5NDG|1|1|A|66
5NDG|1|1|A|67
5NDG|1|1|C|68
*
5NDG|1|1|G|75
5NDG|1|1|G|76
5NDG|1|1|A|77
5NDG|1|1|U|78
5NDG|1|1|U|79
*
5NDG|1|1|A|106
5NDG|1|1|A|107
5NDG|1|1|A|108
5NDG|1|1|A|109
5NDG|1|1|G|110
*
5NDG|1|1|C|321
5NDG|1|1|U|322
5NDG|1|1|A|323
5NDG|1|1|A|324
5NDG|1|1|A|325
5NDG|1|1|U|326
5NDG|1|1|A|327
5NDG|1|1|U|328
5NDG|1|1|U|329
5NDG|1|1|G|330
5NDG|1|1|G|331
*
5NDG|1|4|C|32
5NDG|1|4|A|33
5NDG|1|4|U|34
5NDG|1|4|C|35

Current chains

Chain 1

25S ribosomal RNA

Chain 4

5.8S ribosomal RNA

Nearby chains

Chain L4

60S ribosomal protein L4-A

Chain M3

60S ribosomal protein L13-A

Chain M5

60S ribosomal protein L15-A

Chain O5

60S ribosomal protein L35-A

Chain O6

60S ribosomal protein L36-A

Chain O7

60S ribosomal protein L37-A