J3_5FDV_062

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_062 not in the Motif Atlas

Homologous match to J3_9DFE_013

Geometric discrepancy: 0.0605

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|2A|G|1424
5FDV|1|2A|G|1425
5FDV|1|2A|G|1426
5FDV|1|2A|A|1427
5FDV|1|2A|C|1428
5FDV|1|2A|G|1429
*
5FDV|1|2A|C|1564
5FDV|1|2A|C|1565
*
5FDV|1|2A|G|1568
5FDV|1|2A|A|1569
5FDV|1|2A|A|1570
5FDV|1|2A|A|1571
5FDV|1|2A|A|1572
5FDV|1|2A|G|1573
5FDV|1|2A|C|1574

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2