IL_5NDG_159

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

GUA*UAAC

Length

7 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

IL_5NDG_159 not in the Motif Atlas

Geometric match to IL_4V88_411

Geometric discrepancy: 0.0904

The information below is about IL_4V88_411

Detailed Annotation

Minor groove platform with extra cWW

Broad Annotation

Minor groove platform

Motif group

IL_46796.2

Basepair signature

cWW-tHS-cWW-cWW

Number of instances in this motif group

6

Unit IDs

5NDG|1|2|G|516
5NDG|1|2|U|517
5NDG|1|2|A|518
*
5NDG|1|2|U|533
5NDG|1|2|A|534
5NDG|1|2|A|535
5NDG|1|2|C|536

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain D4

40S ribosomal protein S24-A

Chain S9

40S ribosomal protein S9-A