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Ternary BACE2 xaperone complex

Analyse Ternary 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: 3ZKX
Type: protein
Length: 592 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 2; XA4813; XA4815
EC: 3.4.23.45
UniProt: Q9Y5Z0
Ligands: CL
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 2 (EC 3.4.23.45)	protein	370	14% helix, 43% strand	Q9Y5Z0
B	XA4813	protein	111	5% helix, 50% strand	—
C	XA4815	protein	111	3% helix, 51% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains A, B
DMS · Dimethyl sulfoxide · additive · chains B

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

Pockets

3 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	339	0.66	0.81	43	empty
2	162	0.45	0.76	23	empty
3	61	0.35	0.78	15	empty

Interfaces

2 interfaces between chains.

A–B · 890 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 584 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

3ZKX · Ternary 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 1.00

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 3ZKX · PDBe 3ZKX · UniProt Q9Y5Z0

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