J3_5FDV_059

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

UAAAC*GGGUCGUG*CG

Length

15 nucleotides

Bulged bases

5FDV|1|2A|U|272|||A

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_059 not in the Motif Atlas

Homologous match to J3_9DFE_005

Geometric discrepancy: 0.1201

The information below is about J3_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_97971.2

Basepair signature

cWW-F-F-tSH-cSH-tWH-tWS-cWW-F-cWW

Number of instances in this motif group

3

Unit IDs

5FDV|1|2A|U|269
5FDV|1|2A|A|270
5FDV|1|2A|A|271
5FDV|1|2A|A|271|||A
5FDV|1|2A|C|271|||B
*
5FDV|1|2A|G|271|||V
5FDV|1|2A|G|271|||W
5FDV|1|2A|G|271|||X
5FDV|1|2A|U|271|||Y
5FDV|1|2A|C|271|||Z
5FDV|1|2A|G|272
5FDV|1|2A|U|272|||A
5FDV|1|2A|G|272|||B
*
5FDV|1|2A|C|366
5FDV|1|2A|G|370

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2I

50S ribosomal protein L9