MolNFT v1 · #84434 · protein

BACE2 Fab inhibitor complex

3ZKN · Beta-secretase 2: “BACE2 Fab inhibitor complex”. X-ray diffraction, 2 ligands (WZV, SO4), 14 pockets (best druggability 0.68). MolNFT v1 #84434 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3ZKN
Type: protein
Length: 1,616 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 2; Fab heavy chain; Fab light chain
EC: 3.4.23.45
UniProt: Q9Y5Z0
Ligands: WZV, SO4
Pockets: 14 · best druggability 0.68

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-secretase 2 (EC 3.4.23.45)	protein	375	15% helix, 44% strand	Q9Y5Z0
C, H	Fab heavy chain	protein	216	6% helix, 54% strand	—
D, L	Fab light chain	protein	217	6% helix, 52% strand	—

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	574	0.68	0.78	47	WZV, SO4
2	567	0.68	0.78	43	WZV, SO4
3	438	0.57	0.74	53	empty
4	424	0.57	0.74	53	empty
5	173	0.47	0.76	25	empty

Interfaces

6 interfaces between chains.

H–L · 1857 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1851 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 828 Å² buried · 11 hydrogen bonds · protein-protein
A–L · 823 Å² buried · 13 hydrogen bonds · protein-protein
A–H · 443 Å² 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

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