J3_5FDV_063

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

GCC*GCCUAGUGAACC*GAUCAAC

Length

22 nucleotides

Bulged bases

5FDV|1|2A|A|2388, 5FDV|1|2A|U|2390, 5FDV|1|2A|A|2426

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_063 not in the Motif Atlas

Homologous match to J3_9DFE_015

Geometric discrepancy: 0.0483

The information below is about J3_9DFE_015

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_20992.1

Basepair signature

cWW-F-F-cWW-tHW-tHW-F-cWW-F-F-F-F-F

Number of instances in this motif group

5

Unit IDs

5FDV|1|2A|G|2282
5FDV|1|2A|C|2283
5FDV|1|2A|C|2284
*
5FDV|1|2A|G|2384
5FDV|1|2A|C|2385
5FDV|1|2A|C|2386
5FDV|1|2A|U|2387
5FDV|1|2A|A|2388
5FDV|1|2A|G|2389
5FDV|1|2A|U|2390
5FDV|1|2A|G|2391
5FDV|1|2A|A|2392
5FDV|1|2A|A|2393
5FDV|1|2A|C|2394
5FDV|1|2A|C|2395
*
5FDV|1|2A|G|2421
5FDV|1|2A|A|2422
5FDV|1|2A|U|2423
5FDV|1|2A|C|2424
5FDV|1|2A|A|2425
5FDV|1|2A|A|2426
5FDV|1|2A|C|2427

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 20

50S ribosomal protein L27

Chain 21

50S ribosomal protein L28

Chain 26

50S ribosomal protein L33

Chain 28

50S ribosomal protein L35

Chain 2P

50S ribosomal protein L15

Chain 2Z

50S ribosomal protein L25