J4_5FDV_002

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

CGAAG*CGCC*GAG*CGUAG

Length

17 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

J4_5FDV_002 not in the Motif Atlas

Homologous match to J4_9DFE_002

Geometric discrepancy: 0.0485

The information below is about J4_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_71729.5

Basepair signature

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

Number of instances in this motif group

4

Unit IDs

5FDV|1|1A|C|321
5FDV|1|1A|G|322
5FDV|1|1A|A|323
5FDV|1|1A|A|324
5FDV|1|1A|G|325
*
5FDV|1|1A|C|340
5FDV|1|1A|G|341
5FDV|1|1A|C|342
5FDV|1|1A|C|343
*
5FDV|1|1A|G|347
5FDV|1|1A|A|348
5FDV|1|1A|G|349
*
5FDV|1|1A|C|361
5FDV|1|1A|G|362
5FDV|1|1A|U|363
5FDV|1|1A|A|364
5FDV|1|1A|G|365

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 1F

50S ribosomal protein L4

Chain 1Y

50S ribosomal protein L24