BACE2 Fab inhibitor complex

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 49% strand (DSSP).

Ligands and binding sites

• WZV · 5-(2,2,2-Trifluoro-ethoxy)-pyridine-2-carboxylic acid [3-((S)-2-amino-1,4-dimethyl-6-oxo-1,4,5,6-tetrahydro-pyrimidin-4-yl)-phenyl]-amide · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, H
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains C, H

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

Pockets

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

Interfaces

6 interfaces between chains.

• H–L · 1857 Ų buried · 20 hydrogen bonds · protein-protein
• C–D · 1851 Ų buried · 19 hydrogen bonds · protein-protein
• B–D · 828 Ų buried · 11 hydrogen bonds · protein-protein
• A–L · 823 Ų buried · 13 hydrogen bonds · protein-protein
• A–H · 443 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 2 modified (disulfide, cyclization).

Compared structures

• 3ZKN · BACE2 Fab inhibitor complex · the same entry in another collection · chain L against L, TM-score 1.00
• Q9Y5Z0 · AlphaFold monomer V2.0 prediction for beta-secretase 2 (Q9Y5Z0) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q9Y5Z0
• Elsewhere: RCSB PDB 3ZKN · PDBe 3ZKN · UniProt Q9Y5Z0