J3_5FDV_060

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*CGCCAGAGAG*CGUAG

Length

20 nucleotides

Bulged bases

5FDV|1|2A|G|321

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_060 not in the Motif Atlas

Homologous match to J3_9DFE_006

Geometric discrepancy: 0.0544

The information below is about J3_9DFE_006

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_46299.2

Basepair signature

cWW-F-F-F-cHH-cWW-tHS-F-cWW-cSW-tHS-cWW

Number of instances in this motif group

3

Unit IDs

5FDV|1|2A|C|297
5FDV|1|2A|G|298
5FDV|1|2A|A|299
5FDV|1|2A|A|300
5FDV|1|2A|G|301
*
5FDV|1|2A|C|316
5FDV|1|2A|G|317
5FDV|1|2A|C|318
5FDV|1|2A|C|319
5FDV|1|2A|A|320
5FDV|1|2A|G|321
5FDV|1|2A|A|322
5FDV|1|2A|G|323
5FDV|1|2A|A|324
5FDV|1|2A|G|325
*
5FDV|1|2A|C|337
5FDV|1|2A|G|338
5FDV|1|2A|U|339
5FDV|1|2A|A|340
5FDV|1|2A|G|341

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2F

50S ribosomal protein L4

Chain 2Y

50S ribosomal protein L24