Crystal structure of mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PGSA1) with cdp-dag bound

Structure

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

Ligands and binding sites

• OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 14 copies · chains A, B
• FQT · [(2~{S})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-1,4-dihydropyrimidin-3-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-hexanoyloxy-propyl] hexanoate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 4 copies · chains A, B
• SO4 · Sulfate ion · ion · 10 copies · chains A, B
• PGE · Triethylene glycol · additive · chains A
• 1PE · Pentaethylene glycol · 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 · 2489 Ų buried · 17 hydrogen bonds · protein-protein

Compared structures

• 6H59 · Crystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase… · the same entry in another collection · chain A against A, TM-score 1.00
• P9WPG7 · AlphaFold monomer V2.0 prediction for phosphatidylinositol phosphate synthase (P9WPG7) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P9WPG7
• Elsewhere: RCSB PDB 6H59 · PDBe 6H59 · UniProt P9WPG7