IL_5FDV_070

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

UGCGAAC*GGAGGUAUA

Length

16 nucleotides

Bulged bases

5FDV|1|1A|G|1832, 5FDV|1|1A|G|1847, 5FDV|1|1A|U|1851

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

IL_5FDV_070 not in the Motif Atlas

Homologous match to IL_7RQB_070

Geometric discrepancy: 0.0401

The information below is about IL_7RQB_070

Detailed Annotation

Kink-turn related

Broad Annotation

No text annotation

Motif group

IL_17069.3

Basepair signature

cWW-tSH-tHH-cSS-tWW-tHH-tSS-cWW

Number of instances in this motif group

5

Unit IDs

5FDV|1|1A|U|1829
5FDV|1|1A|G|1830
5FDV|1|1A|C|1831
5FDV|1|1A|G|1832
5FDV|1|1A|A|1833
5FDV|1|1A|A|1834
5FDV|1|1A|C|1835
*
5FDV|1|1A|G|1844
5FDV|1|1A|G|1845
5FDV|1|1A|A|1846
5FDV|1|1A|G|1847
5FDV|1|1A|G|1848
5FDV|1|1A|U|1849
5FDV|1|1A|A|1850
5FDV|1|1A|U|1851
5FDV|1|1A|A|1852

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 1D

50S ribosomal protein L2

Chain 1a

Small subunit ribosomal RNA; SSU rRNA