Crystal structure of the super-active fviia variant vyt in complex with tissue factor

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 37% strand (DSSP).

Ligands and binding sites

• 0Z7 · N-acetyl-D-phenylalanyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide · ligand · chains H
• XYS · alpha-D-xylopyranose · sugar · 2 copies · chains L, T
• BGC · beta-D-glucopyranose · sugar · chains L
• FUC · alpha-L-fucopyranose · sugar · chains L, T
• CA · Calcium ion · metal · 9 copies · chains L, H
• TMA · Tetramethylammonium ion · additive · 10 copies · chains L, T, H

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• L–T · 1434 Ų buried · 16 hydrogen bonds · protein-protein
• L–H · 1041 Ų buried · 13 hydrogen bonds · protein-protein
• H–T · 768 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 10 modified, 2 covalent, 2 glycan (disulfide, carboxylation, covalent ligand, O-glycosylation).

Compared structures

• 6R2W · Crystal structure of the super-active FVIIa variant VYT in complex with tissue factor · the same entry in another collection · chain L against L, TM-score 1.00
• P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain H 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 P08709
• Every structure of UniProt P13726
• Elsewhere: RCSB PDB 6R2W · PDBe 6R2W · UniProt P08709 · UniProt P13726