J3_5FDV_049

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

CGG*CUAG*CG

Length

9 nucleotides

Bulged bases

5FDV|1|1a|A|653

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_049 not in the Motif Atlas

Geometric match to J3_4LFB_011

Geometric discrepancy: 0.1065

The information below is about J3_4LFB_011

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_56052.5

Basepair signature

cWW-F-cWW-cWW-F

Number of instances in this motif group

5

Unit IDs

5FDV|1|1a|C|586
5FDV|1|1a|G|587
5FDV|1|1a|G|588
*
5FDV|1|1a|C|651
5FDV|1|1a|U|652
5FDV|1|1a|A|653
5FDV|1|1a|G|654
*
5FDV|1|1a|C|754
5FDV|1|1a|G|755

Current chains

Chain 1a

16S ribosomal RNA

Nearby chains

Chain 1h

30S ribosomal protein S8

Chain 1l

30S ribosomal protein S12

Chain 1o

30S ribosomal protein S15

Chain 1q

30S ribosomal protein S17