J4_5FDV_020

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

GACUG*CACAG*CGAC*GUAAC

Length

19 nucleotides

Bulged bases

None detected

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_020 not in the Motif Atlas

Homologous match to J4_9DFE_007

Geometric discrepancy: 0.0444

The information below is about J4_9DFE_007

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61477.5

Basepair signature

cWW-tSW-F-tHS-tHS-F-cWW-cWW-F-tHS-cWW

Number of instances in this motif group

4

Unit IDs

5FDV|1|2A|G|1772
5FDV|1|2A|A|1773
5FDV|1|2A|C|1774
5FDV|1|2A|U|1775
5FDV|1|2A|G|1776
*
5FDV|1|2A|C|1788
5FDV|1|2A|A|1789
5FDV|1|2A|C|1790
5FDV|1|2A|A|1791
5FDV|1|2A|G|1792
*
5FDV|1|2A|C|1827
5FDV|1|2A|G|1828
5FDV|1|2A|A|1829
5FDV|1|2A|C|1830
*
5FDV|1|2A|G|1975
5FDV|1|2A|U|1976
5FDV|1|2A|A|1977
5FDV|1|2A|A|1978
5FDV|1|2A|C|1979

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA