IL_5NDW_101

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

GUG*UUUUU

Length

8 nucleotides

Bulged bases

5NDW|1|1|U|2860

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_101 not in the Motif Atlas

Geometric match to IL_5TBW_105

Geometric discrepancy: 0.0799

The information below is about IL_5TBW_105

Detailed Annotation

Major groove minor groove platform with extra cWW

Broad Annotation

Major groove minor groove platform with extra cWW

Motif group

IL_63959.1

Basepair signature

cWW-cSH-cWW-cWW

Number of instances in this motif group

18

Unit IDs

5NDW|1|1|G|2828
5NDW|1|1|U|2829
5NDW|1|1|G|2830
*
5NDW|1|1|U|2858
5NDW|1|1|U|2859
5NDW|1|1|U|2860
5NDW|1|1|U|2861
5NDW|1|1|U|2862

Current chains

Chain 1

25S ribosomal RNA

Nearby chains

Chain L3

60S ribosomal protein L3

Chain M0

60S ribosomal protein L10