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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: 3ZLQ
Type: protein
Length: 961 residues
Chains: 4
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: 6T9
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 2 (EC 3.4.23.45)	protein	367	14% helix, 43% strand	Q9Y5Z0
B	Beta-secretase 2 (EC 3.4.23.45)	protein	370	15% helix, 44% strand	Q9Y5Z0
C, D	XA4813	protein	112	11% helix, 50% strand	—

Ligands and binding sites

6T9 · 5-Ethoxy-pyridine-2-carboxylic acid [3-((R)-2-amino-5,5-difluoro-4-methyl-5,6-dihydro-4H-[1,3]oxazin-4-yl)-4-fluoro-phenyl]-amide · ligand · 2 copies · chains A, B

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

Pockets

6 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	988	0.75	0.78	77	6T9
2	1045	0.74	0.77	74	6T9
3	180	0.50	0.77	24	empty
4	154	0.44	0.76	20	empty
5	50	0.32	0.77	16	empty

Interfaces

3 interfaces between chains.

B–D · 852 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 841 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 768 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3ZLQ · 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 0.98

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 3ZLQ · PDBe 3ZLQ · UniProt Q9Y5Z0

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