J4_5FDV_021

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

UUG*CG*CCUAAGGUAG*CGAAAA

Length

21 nucleotides

Bulged bases

5FDV|1|2A|A|1971

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_021 not in the Motif Atlas

Homologous match to J4_9DFE_008

Geometric discrepancy: 0.0477

The information below is about J4_9DFE_008

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_93343.1

Basepair signature

cWW-tSS-cSS-cWH-cWW-tWH-tHS-cWW-cWW-tWW-F-cSH-F-F

Number of instances in this motif group

4

Unit IDs

5FDV|1|2A|U|1833
5FDV|1|2A|U|1834
5FDV|1|2A|G|1835
*
5FDV|1|2A|C|1905
5FDV|1|2A|G|1906
*
5FDV|1|2A|C|1924
5FDV|1|2A|C|1925
5FDV|1|2A|U|1926
5FDV|1|2A|A|1927
5FDV|1|2A|A|1928
5FDV|1|2A|G|1929
5FDV|1|2A|G|1930
5FDV|1|2A|U|1931
5FDV|1|2A|A|1932
5FDV|1|2A|G|1933
*
5FDV|1|2A|C|1967
5FDV|1|2A|G|1968
5FDV|1|2A|A|1969
5FDV|1|2A|A|1970
5FDV|1|2A|A|1971
5FDV|1|2A|A|1972

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA