J3_5FDV_027

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

CUAG*CGAAG*CGUUAAG

Length

16 nucleotides

Bulged bases

5FDV|1|2a|U|871, 5FDV|1|2a|A|873

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_027 not in the Motif Atlas

Homologous match to J3_4LFB_001

Geometric discrepancy: 0.0591

The information below is about J3_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_85054.4

Basepair signature

cWW-tWW-tHS-F-cWW-tHS-cWW-F

Number of instances in this motif group

3

Unit IDs

5FDV|1|2a|C|826
5FDV|1|2a|U|827
5FDV|1|2a|A|828
5FDV|1|2a|G|829
*
5FDV|1|2a|C|857
5FDV|1|2a|G|858
5FDV|1|2a|A|859
5FDV|1|2a|A|860
5FDV|1|2a|G|861
*
5FDV|1|2a|C|868
5FDV|1|2a|G|869
5FDV|1|2a|U|870
5FDV|1|2a|U|871
5FDV|1|2a|A|872
5FDV|1|2a|A|873
5FDV|1|2a|G|874

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2b

30S ribosomal protein S2

Chain 2h

30S ribosomal protein S8