J3_5FDV_023

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

CAAG*CGCAAAC*GUG

Length

14 nucleotides

Bulged bases

5FDV|1|2A|A|1609

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

J3_5FDV_023 not in the Motif Atlas

Homologous match to J3_7RQB_008

Geometric discrepancy: 0.0396

The information below is about J3_7RQB_008

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_16623.1

Basepair signature

cWW-tSH-tWW-tHH-F-tHW-cWW-F-cWW

Number of instances in this motif group

2

Unit IDs

5FDV|1|2A|C|1306
5FDV|1|2A|A|1307
5FDV|1|2A|A|1308
5FDV|1|2A|G|1309
*
5FDV|1|2A|C|1605
5FDV|1|2A|G|1606
5FDV|1|2A|C|1607
5FDV|1|2A|A|1608
5FDV|1|2A|A|1609
5FDV|1|2A|A|1610
5FDV|1|2A|C|1611
*
5FDV|1|2A|G|1620
5FDV|1|2A|U|1621
5FDV|1|2A|G|1622

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 27

50S ribosomal protein L34