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MolNFT v1 · #89640 · protein

Crystal structure of BACE1 with its inhibitor

4DV9 · Beta-secretase 1: “Crystal structure of BACE1 with its inhibitor”. X-ray diffraction, 2 ligands (2OP, SO4). MolNFT v1 #89640 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4DV9
Type
protein
Length
386 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Beta-secretase 1; Methyl (2S)-1-[(2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-amino…
EC
3.4.23.46
UniProt
P56817
Ligands
2OP, SO4

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABeta-secretase 1 (EC 3.4.23.46)protein37916% helix, 41% strandP56817
BMethyl (2S)-1-[(2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-amino- 3-oxopropyl)-2,13-dibenzyl-12,22-dihydroxy-3,5,17-trimethyl-8-(2- methylpropyl)-4,7,10,15,18,21-hexaoxo-19-(propan-2-yl)-3,6,9,14,17, 20-hexaazatricosan-1-OYL]PYRROLIDINE-2-carboxylate (non-preferred name)protein70% helix, 29% strand—

Ligands and binding sites

  • 2OP · (2S)-2-hydroxypropanoic acid · ligand · chains A, B
  • SO4 · Sulfate ion · ion · 4 copies · chains A

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

Interfaces

1 interface between chains.

  • A–B · 761 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 3 disulfide, 1 covalent (nonstandard, disulfide, covalent ligand).

Compared structures

  • 4DV9 · Crystal structure of BACE1 with its inhibitor · 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 A against A, TM-score 0.98

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