Crystal structure of the endothelial protein C receptor with phospholipid in the groove in complex with gla domain of protein C.

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 34% strand (DSSP).

Ligands and binding sites

• PTY · Phosphatidylethanolamine · ligand · 2 copies · chains A, C, B, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
• CA · Calcium ion · metal · 14 copies · chains A, C, B, D

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

3 interfaces between chains.

• A–C · 489 Ų buried · 9 hydrogen bonds · protein-protein
• B–D · 487 Ų buried · 10 hydrogen bonds · protein-protein
• A–B · 45 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 18 modified, 6 glycan, 4 disulfide (carboxylation, N-glycosylation, disulfide).

Compared structures

• 1LQV · Crystal structure of the Endothelial protein C receptor with phospholipid in the groove… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9UNN8 · AlphaFold monomer V2.0 prediction for endothelial protein C receptor (Q9UNN8) · a predicted model of the same protein · chain A against A, TM-score 1.00
• P04070 · AlphaFold monomer V2.0 prediction for vitamin K-dependent protein C (P04070) · a predicted model of the same protein · chain C against A, TM-score 0.85

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 Q9UNN8
• Every structure of UniProt P04070
• Elsewhere: RCSB PDB 1LQV · PDBe 1LQV · UniProt Q9UNN8 · UniProt P04070