J3_5FDV_042

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

GCGGGAC*GGCAG*CC

Length

14 nucleotides

Bulged bases

5FDV|1|1A|A|1430

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_042 not in the Motif Atlas

Homologous match to J3_9DFE_012

Geometric discrepancy: 0.0537

The information below is about J3_9DFE_012

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_31965.2

Basepair signature

cWW-F-cWW-F-F-F-F-F-cWW-F

Number of instances in this motif group

6

Unit IDs

5FDV|1|1A|G|1390
5FDV|1|1A|C|1391
5FDV|1|1A|G|1392
5FDV|1|1A|G|1393
5FDV|1|1A|G|1394
5FDV|1|1A|A|1395
5FDV|1|1A|C|1396
*
5FDV|1|1A|G|1427
5FDV|1|1A|G|1428
5FDV|1|1A|C|1429
5FDV|1|1A|A|1430
5FDV|1|1A|G|1431
*
5FDV|1|1A|C|1448
5FDV|1|1A|C|1449

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 1X

50S ribosomal protein L23