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Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of glycerol 3-phosphate

Analyse Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8AVT
Type: protein
Length: 204 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.2
Molecule: D-Aureocin A53
Ligands: G3P
Pockets: 1 · best druggability 0.32

Structure

x-ray diffraction · resolution 1.2 · 1 distinct chain · 82% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D, B, A	D-Aureocin A53	protein	51	82% helix, 0% strand	—

Ligands and binding sites

G3P · Sn-glycerol-3-phosphate · ligand · 2 copies · chains D, A
EDO · 1,2-ethanediol · additive · 5 copies · chains C, D, B
PEG · Di(hydroxyethyl)ether · additive · chains C
GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	72	0.32	0.74	13	empty

Interfaces

3 interfaces between chains.

C–D · 272 Å² buried · 1 hydrogen bond · protein-protein
C–B · 239 Å² buried · 2 hydrogen bonds · protein-protein
B–A · 207 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 94 d-amino (D-amino acid).

Compared structures

Q8GPI4 · AlphaFold monomer V2.0 prediction for bacteriocin aureocin A53 (Q8GPI4) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8AVT · PDBe 8AVT

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