MolNFT v1 · #84428 · protein

BACE2 mutant apo structure

3ZKG · Beta-secretase 2: “BACE2 mutant apo structure”. X-ray diffraction, 4 pockets (best druggability 0.71). MolNFT v1 #84428 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3ZKG
Type: protein
Length: 723 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 2
EC: 3.4.23.45
UniProt: Q9Y5Z0
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 2 (EC 3.4.23.45)	protein	364	16% helix, 46% strand	Q9Y5Z0
B	Beta-secretase 2 (EC 3.4.23.45)	protein	359	14% helix, 44% strand	Q9Y5Z0

Ligands and binding sites

B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	778	0.71	0.77	71	B3P
2	677	0.68	0.76	63	empty
3	120	0.48	0.79	21	empty
4	57	0.31	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 425 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3ZKG · BACE2 mutant apo structure · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y5Z0 · AlphaFold monomer V2.0 prediction for beta-secretase 2 (Q9Y5Z0) · a predicted model of the same protein · chain A 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 Q9Y5Z0
Elsewhere: RCSB PDB 3ZKG · PDBe 3ZKG · UniProt Q9Y5Z0

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