Crystal structure of phosphatidyl serine synthase (pss) in the closed conformation with bound citrate.

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 2% strand (DSSP).

Ligands and binding sites

• 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
• CA · Calcium ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 4 copies · chains A, B
• OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 6 copies · chains A, B
• FLC · Citrate anion · additive · 3 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 2044 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

• 7B1K · Crystal structure of phosphatidyl serine synthase (PSS) in the closed conformation with… · the same entry in another collection · chain A against A, TM-score 1.00
• Q58609 · AlphaFold monomer V2.0 prediction for cdp-diacylglycerol--serine… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q58609
• Elsewhere: RCSB PDB 7B1K · PDBe 7B1K · UniProt Q58609