J3_5FDV_056

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

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

5FDV|1|2A|U|504, 5FDV|1|2A|G|508

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_056 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.0471

The information below is about J3_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_92134.2

Basepair signature

cWW-cWW-cWW-F-tWH-cSS-tSS-tSH-tSH-tWW-tHH-tWH-tWW-F-F-cSS-cSW-F-tHS-cWW

Number of instances in this motif group

6

Unit IDs

5FDV|1|2A|G|30
5FDV|1|2A|C|31
*
5FDV|1|2A|G|474
5FDV|1|2A|U|475
5FDV|1|2A|G|476
5FDV|1|2A|A|477
5FDV|1|2A|A|478
5FDV|1|2A|A|479
5FDV|1|2A|A|480
5FDV|1|2A|G|481
5FDV|1|2A|A|482
5FDV|1|2A|A|483
5FDV|1|2A|C|484
*
5FDV|1|2A|G|496
5FDV|1|2A|A|497
5FDV|1|2A|G|498
5FDV|1|2A|U|499
5FDV|1|2A|G|500
5FDV|1|2A|A|501
5FDV|1|2A|A|502
5FDV|1|2A|A|503
5FDV|1|2A|U|504
5FDV|1|2A|A|505
5FDV|1|2A|G|506
5FDV|1|2A|A|507
5FDV|1|2A|G|508
5FDV|1|2A|C|509
5FDV|1|2A|C|510

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2U

50S ribosomal protein L20

Chain 2W

50S ribosomal protein L22

Chain 2Y

50S ribosomal protein L24