IL_5FDV_244

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|2A|G|1801, 5FDV|1|2A|G|1816, 5FDV|1|2A|U|1820

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_244 not in the Motif Atlas

Homologous match to IL_7RQB_070

Geometric discrepancy: 0.0453

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|2A|U|1798
5FDV|1|2A|G|1799
5FDV|1|2A|C|1800
5FDV|1|2A|G|1801
5FDV|1|2A|A|1802
5FDV|1|2A|A|1803
5FDV|1|2A|C|1804
*
5FDV|1|2A|G|1813
5FDV|1|2A|G|1814
5FDV|1|2A|A|1815
5FDV|1|2A|G|1816
5FDV|1|2A|G|1817
5FDV|1|2A|U|1818
5FDV|1|2A|A|1819
5FDV|1|2A|U|1820
5FDV|1|2A|A|1821

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA