Crystal structure of phosphatidylglycerol phosphate synthase in complex with phosphatidylglycerol phosphate

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 3% strand (DSSP).

Ligands and binding sites

• PO9 · [(2R)-2-hexadecanoyloxy-3-[oxidanyl-[(2S)-2-oxidanyl-3-phosphonooxy-propoxy]phosphoryl]oxy-propyl] (Z)-octadec-9-enoate · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• BU1 · 1,4-butanediol · additive · 14 copies · chains A, B
• OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A, B
• ACY · Acetic acid · additive · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1419 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 7DRJ · Crystal structure of phosphatidylglycerol phosphate synthase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• P63756 · AlphaFold monomer V2.0 prediction for cdp-diacylglycerol-- glycerol-3-phosphate… · a predicted model of the same protein · chain A against A, TM-score 0.90

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 P63756
• Elsewhere: RCSB PDB 7DRJ · PDBe 7DRJ · UniProt P63756