Crystal structure of LECITHIN:CHOLESTEROL acyltransferase (lcat) in complex with isopropyl dodec-11-enylfluorophosphonate (idfp) and a small molecule activator

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).

Ligands and binding sites

• H9A · propan-2-yl hydrogen (R)-ethylphosphonate · ligand · 2 copies · chains A, B
• H94 · 6-{4-[(4R)-4-hydroxy-6-oxo-4-(trifluoromethyl)-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-b]pyridin-3-yl]piperidin-1-yl}-4-(trifluoromethyl)pyridine-3-carbonitrile · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
• NI · Nickel (II) ion · metal · chains A
• SO4 · Sulfate ion · ion · 6 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 602 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 5 glycan, 4 disulfide, 2 covalent (N-glycosylation, disulfide, covalent ligand).

Compared structures

• 6MVD · Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• P04180 · AlphaFold monomer V2.0 prediction for phosphatidylcholine-sterol acyltransferase (P04180) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P04180
• Elsewhere: RCSB PDB 6MVD · PDBe 6MVD · UniProt P04180