IL_5FDV_173

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

GGAG*UGAC

Length

8 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

IL_5FDV_173 not in the Motif Atlas

Homologous match to IL_5J7L_062

Geometric discrepancy: 0.0672

The information below is about IL_5J7L_062

Detailed Annotation

Double sheared

Broad Annotation

Double sheared

Motif group

IL_09705.15

Basepair signature

cWW-tSH-tHS-cWW

Number of instances in this motif group

34

Unit IDs

5FDV|1|1a|G|1416
5FDV|1|1a|G|1417
5FDV|1|1a|A|1418
5FDV|1|1a|G|1419
*
5FDV|1|1a|U|1481
5FDV|1|1a|G|1482
5FDV|1|1a|A|1483
5FDV|1|1a|C|1484

Current chains

Chain 1a

16S ribosomal RNA

Nearby chains

Chain 1A

Large subunit ribosomal RNA; LSU rRNA