IL_5FDV_314

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

CGGCCAAC*GG

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_314 not in the Motif Atlas

Homologous match to IL_4LFB_020

Geometric discrepancy: 0.0982

The information below is about IL_4LFB_020

Detailed Annotation

SSU/LSU pseudoknot

Broad Annotation

No text annotation

Motif group

IL_41203.4

Basepair signature

cWW-L-cWW-L-L-R-cSH

Number of instances in this motif group

11

Unit IDs

5FDV|1|2a|C|504
5FDV|1|2a|G|505
5FDV|1|2a|G|506
5FDV|1|2a|C|507
5FDV|1|2a|C|508
5FDV|1|2a|A|509
5FDV|1|2a|A|510
5FDV|1|2a|C|511
*
5FDV|1|2a|G|540
5FDV|1|2a|G|541

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2d

30S ribosomal protein S4

Chain 2e

30S ribosomal protein S5

Chain 2l

30S ribosomal protein S12