IL_5FDV_027

3D structure

PDB id

5FDV (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Pyrrhocoricin antimicrobial peptide bound to the Thermus thermophilus 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

UGUAG*CGAAG

Length

10 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_5FDV_027 not in the Motif Atlas

Homologous match to IL_7RQB_027

Geometric discrepancy: 0.0423

The information below is about IL_7RQB_027

Detailed Annotation

5x5 Sarcin-Ricin with intercalated A; G-bulge

Broad Annotation

Sarcin-Ricin; G-bulge

Motif group

IL_38862.1

Basepair signature

cWW-L-R-tWH-tHS-cWW

Number of instances in this motif group

4

Unit IDs

5FDV|1|1A|U|905
5FDV|1|1A|G|906
5FDV|1|1A|U|907
5FDV|1|1A|A|908
5FDV|1|1A|G|909
*
5FDV|1|1A|C|961
5FDV|1|1A|G|962
5FDV|1|1A|A|963
5FDV|1|1A|A|964
5FDV|1|1A|G|965

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 10

50S ribosomal protein L27

Chain 1B

5S ribosomal RNA; 5S rRNA

Chain 1Q

50S ribosomal protein L16