J3_5NDW_017

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

AGAG*CAG*UCGAAU

Length

13 nucleotides

Bulged bases

None detected

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_017 not in the Motif Atlas

Homologous match to J3_4V88_032

Geometric discrepancy: 0.0767

The information below is about J3_4V88_032

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_54972.1

Basepair signature

cWW-tWW-F-cWW-F-tHS-F-cWW

Number of instances in this motif group

2

Unit IDs

5NDW|1|2|A|760
5NDW|1|2|G|761
5NDW|1|2|A|762
5NDW|1|2|G|763
*
5NDW|1|2|C|773
5NDW|1|2|A|774
5NDW|1|2|G|775
*
5NDW|1|2|U|785
5NDW|1|2|C|786
5NDW|1|2|G|787
5NDW|1|2|A|788
5NDW|1|2|A|789
5NDW|1|2|U|790

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain D4

40S ribosomal protein S24-A

Chain S4

40S ribosomal protein S4-A

Chain S9

40S ribosomal protein S9-A