Crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with (2S)-2-((3S)-3-(acetylamino)-3-(butan-2-yl)-2-oxopyrrolidin-1- yl)-N-((2S,3R)-3-hydroxy-4-((3-METHOXYBENZYL)AMINO)-1-phenylbutan-2- yl)-4-phenylbutanamide

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 39% strand (DSSP).

Ligands and binding sites

• PB7 · (2S)-2-{(3S)-3-(acetylamino)-3-[(2S)-butan-2-yl]-2-oxopyrrolidin-1-yl}-N-{(2S,3R)-3-hydroxy-4-[(3-methoxybenzyl)amino]-1-phenylbutan-2-yl}-4-phenylbutanamide · ligand · 2 copies · chains A, B
• IOD · Iodide ion · ion · 2 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, 6 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 825 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 3SKF · Crystal structure of beta-site app-cleaving enzyme 1 (BACE-WT) complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P56817
• Elsewhere: RCSB PDB 3SKF · PDBe 3SKF · UniProt P56817