IL_5FDV_356

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

CGGGAG*CAG

Length

9 nucleotides

Bulged bases

5FDV|1|2a|G|1442|||A

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_356 not in the Motif Atlas

Homologous match to IL_6CZR_172

Geometric discrepancy: 0.1077

The information below is about IL_6CZR_172

Detailed Annotation

Isolated basepair with bulged bases

Broad Annotation

Isolated basepair with bulged bases

Motif group

IL_97255.3

Basepair signature

cWW-tSH-L-cWW-L

Number of instances in this motif group

5

Unit IDs

5FDV|1|2a|C|1440
5FDV|1|2a|G|1441
5FDV|1|2a|G|1442
5FDV|1|2a|G|1442|||A
5FDV|1|2a|A|1442|||B
5FDV|1|2a|G|1443
*
5FDV|1|2a|C|1459
5FDV|1|2a|A|1460
5FDV|1|2a|G|1461

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2A

Large subunit ribosomal RNA; LSU rRNA

Chain 2T

50S ribosomal protein L19

Chain 2t

30S ribosomal protein S20