Crystal structure of phosphatidylglycerol phosphate synthase in complex with cytidine diphosphate-diacylglycerol

Structure

x-ray diffraction · 2 distinct chains · 76% helix, 2% strand (DSSP).

Ligands and binding sites

• G3P · Sn-glycerol-3-phosphate · ligand · 5 copies · chains A
• 58A · 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9e)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy) phosphoryl]cytidine · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• BU1 · 1,4-butanediol · additive · 10 copies · chains B
• OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 3 copies · chains A, B
• ACY · Acetic acid · additive · 2 copies · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1392 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 7DRK · Crystal structure of phosphatidylglycerol phosphate synthase in complex with cytidine… · 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 7DRK · PDBe 7DRK · UniProt P63756