J3_5FDV_043

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

GGGACG*CC*GAAAAGC

Length

15 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

J3_5FDV_043 not in the Motif Atlas

Homologous match to J3_9DFE_013

Geometric discrepancy: 0.047

The information below is about J3_9DFE_013

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_34864.2

Basepair signature

cWW-F-cWW-F-tHH-F-tHS-tHS-cWW

Number of instances in this motif group

4

Unit IDs

5FDV|1|1A|G|1470
5FDV|1|1A|G|1471
5FDV|1|1A|G|1472
5FDV|1|1A|A|1473
5FDV|1|1A|C|1474
5FDV|1|1A|G|1475
*
5FDV|1|1A|C|1611
5FDV|1|1A|C|1612
*
5FDV|1|1A|G|1615
5FDV|1|1A|A|1616
5FDV|1|1A|A|1617
5FDV|1|1A|A|1618
5FDV|1|1A|A|1619
5FDV|1|1A|G|1620
5FDV|1|1A|C|1621

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 1D

50S ribosomal protein L2