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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: 4BFB
Type: protein
Length: 978 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
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 13% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 2 (EC 3.4.23.45)	protein	373	14% helix, 42% strand	Q9Y5Z0
B	Beta-secretase 2 (EC 3.4.23.45)	protein	374	13% helix, 42% strand	Q9Y5Z0
D	XA4813	protein	110	11% helix, 52% strand	—
E	XA4813	protein	121	7% helix, 47% strand	—

Ligands and binding sites

B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1026	0.74	0.77	100	empty
2	492	0.67	0.78	44	empty
3	519	0.67	0.77	40	B3P
4	172	0.60	0.83	30	empty
5	149	0.44	0.75	20	empty

Interfaces

5 interfaces between chains.

A–E · 854 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 848 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 773 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 491 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 132 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4BFB · 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 B 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 4BFB · PDBe 4BFB · UniProt Q9Y5Z0

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