J4_5FDV_022

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

CAAAG*CUGAC*GGG*CGG

Length

16 nucleotides

Bulged bases

5FDV|1|2A|A|2288

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_022 not in the Motif Atlas

Homologous match to J4_9DFE_009

Geometric discrepancy: 0.0625

The information below is about J4_9DFE_009

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_04930.6

Basepair signature

cWW-F-F-tWW-tHH-cWW-cWW-cHW-cWW

Number of instances in this motif group

7

Unit IDs

5FDV|1|2A|C|2285
5FDV|1|2A|A|2286
5FDV|1|2A|A|2287
5FDV|1|2A|A|2288
5FDV|1|2A|G|2289
*
5FDV|1|2A|C|2343
5FDV|1|2A|U|2344
5FDV|1|2A|G|2345
5FDV|1|2A|A|2346
5FDV|1|2A|C|2347
*
5FDV|1|2A|G|2370
5FDV|1|2A|G|2371
5FDV|1|2A|G|2372
*
5FDV|1|2A|C|2381
5FDV|1|2A|G|2382
5FDV|1|2A|G|2383

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 20

50S ribosomal protein L27

Chain 26

50S ribosomal protein L33

Chain 28

50S ribosomal protein L35

Chain 2S

50S ribosomal protein L18