Human coagulation factor xiia (fxiia) bound with the macrocyclic peptide F3 containing two (1S,2S)-2-achc residues

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 34% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · 2 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• C–D · 867 Ų buried · 23 hydrogen bonds · protein-protein
• A–B · 867 Ų buried · 22 hydrogen bonds · protein-protein
• A–C · 551 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 covalent, 4 d-amino, 4 modified, 2 glycan (disulfide, covalent ligand, D-amino acid, nonstandard, N-glycosylation).

Compared structures

• 6L63 · Human Coagulation Factor XIIa (FXIIa) bound with the macrocyclic peptide F3 containing… · the same entry in another collection · chain A against A, TM-score 1.00
• P00748 · AlphaFold monomer V2.0 prediction for coagulation factor XII (P00748) · 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 P00748
• Elsewhere: RCSB PDB 6L63 · PDBe 6L63 · UniProt P00748