IL_5NDW_240

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

GAC*GU

Length

5 nucleotides

Bulged bases

5NDW|1|5|A|338

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_5NDW_240 not in the Motif Atlas

Homologous match to IL_5TBW_013

Geometric discrepancy: 0.083

The information below is about IL_5TBW_013

Detailed Annotation

Single bulged A

Broad Annotation

No text annotation

Motif group

IL_31462.1

Basepair signature

cWW-L-cWW

Number of instances in this motif group

127

Unit IDs

5NDW|1|5|G|337
5NDW|1|5|A|338
5NDW|1|5|C|339
*
5NDW|1|8|G|25
5NDW|1|8|U|26

Current chains

Chain 5

25S ribosomal RNA

Chain 8

5.8S ribosomal RNA

Nearby chains

Chain l4

60S ribosomal protein L4-A

Chain n6

60S ribosomal protein L26-A