J3_5FDV_020

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

CAG*CGAAC*GAUG

Length

12 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_020 not in the Motif Atlas

Homologous match to J3_7RQB_005

Geometric discrepancy: 0.0439

The information below is about J3_7RQB_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_44724.4

Basepair signature

cWW-tSH-F-cWW-tHS-cWW-F

Number of instances in this motif group

6

Unit IDs

5FDV|1|2A|C|698
5FDV|1|2A|A|699
5FDV|1|2A|G|700
*
5FDV|1|2A|C|732
5FDV|1|2A|G|733
5FDV|1|2A|A|734
5FDV|1|2A|A|735
5FDV|1|2A|C|736
*
5FDV|1|2A|G|760
5FDV|1|2A|A|761
5FDV|1|2A|U|762
5FDV|1|2A|G|763

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2