J3_5FDV_058

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

AC*GAUAAGC*GAUGU

Length

14 nucleotides

Bulged bases

5FDV|1|2A|U|72, 5FDV|1|2A|A|74

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_058 not in the Motif Atlas

Homologous match to J3_9DFE_004

Geometric discrepancy: 0.0533

The information below is about J3_9DFE_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_35667.2

Basepair signature

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

Number of instances in this motif group

7

Unit IDs

5FDV|1|2A|A|56
5FDV|1|2A|C|57
*
5FDV|1|2A|G|70
5FDV|1|2A|A|71
5FDV|1|2A|U|72
5FDV|1|2A|A|73
5FDV|1|2A|A|74
5FDV|1|2A|G|75
5FDV|1|2A|C|76
*
5FDV|1|2A|G|110
5FDV|1|2A|A|111
5FDV|1|2A|U|112
5FDV|1|2A|G|113
5FDV|1|2A|U|114

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 22

50S ribosomal protein L29

Chain 27

50S ribosomal protein L34

Chain 2X

50S ribosomal protein L23