J6_5NDW_001

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

GAGUAC*GGAAAAGAAAC*GGAUU*AAAAG*CUAAAUAUUGG*CAUC

Length

42 nucleotides

Bulged bases

5NDW|1|1|A|67, 5NDW|1|1|U|329, 5NDW|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

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