J4_5FDV_001

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

CU*GAGUAC*GGAAUCUG*UAAG

Length

20 nucleotides

Bulged bases

5FDV|1|1A|U|432

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_001 not in the Motif Atlas

Homologous match to J4_9DFE_001

Geometric discrepancy: 0.0523

The information below is about J4_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_45801.6

Basepair signature

cWW-cWW-cSS-F-tHH-cWW-cSH-tWH-F-tHS-F-cWW

Number of instances in this motif group

7

Unit IDs

5FDV|1|1A|C|257
5FDV|1|1A|U|258
*
5FDV|1|1A|G|397
5FDV|1|1A|A|398
5FDV|1|1A|G|399
5FDV|1|1A|U|400
5FDV|1|1A|A|401
5FDV|1|1A|C|402
*
5FDV|1|1A|G|426
5FDV|1|1A|G|427
5FDV|1|1A|A|428
5FDV|1|1A|A|429
5FDV|1|1A|U|430
5FDV|1|1A|C|431
5FDV|1|1A|U|432
5FDV|1|1A|G|433
*
5FDV|1|1A|U|448
5FDV|1|1A|A|449
5FDV|1|1A|A|450
5FDV|1|1A|G|451

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L28

Chain 1I

50S ribosomal protein L9