Research workbench

BACE2 xaperone complex

Analyse BACE2 xaperone complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZKQ
Type: protein
Length: 489 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 2; XA4813
EC: 3.4.23.45
UniProt: Q9Y5Z0
Ligands: CL
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 2 (EC 3.4.23.45)	protein	376	15% helix, 41% strand	Q9Y5Z0
D	XA4813	protein	113	8% helix, 50% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains A, D
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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	562	0.69	0.78	49	B3P
2	111	0.40	0.76	16	empty
3	92	0.37	0.75	22	empty
4	50	0.26	0.73	16	empty

Interfaces

1 interface between chains.

A–D · 870 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3ZKQ · BACE2 xaperone complex · 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 3ZKQ · PDBe 3ZKQ · UniProt Q9Y5Z0

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