Crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex with ceftobiprole

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).

Ligands and binding sites

• RB6 · (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• NA · Sodium ion · metal · 4 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · chains B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 211 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 5TXI · Crystal structure of wild-type S. aureus penicillin binding protein 4 (PBP4) in complex… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt A0A0H2WY27
• Elsewhere: RCSB PDB 5TXI · PDBe 5TXI · UniProt A0A0H2WY27