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BACE2 Fab complex

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

PDB: 3ZKM
Type: protein
Length: 1,616 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 2; Fab heavy chain; Fab light chain
EC: 3.4.23.45
UniProt: Q9Y5Z0
Ligands: SO4
Pockets: 18 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-secretase 2 (EC 3.4.23.45)	protein	375	15% helix, 43% strand	Q9Y5Z0
C, H	Fab heavy chain	protein	216	6% helix, 54% strand	—
D, L	Fab light chain	protein	217	6% helix, 52% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains C, H

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

Pockets

18 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	377	0.67	0.80	43	empty
2	355	0.66	0.80	39	empty
3	437	0.58	0.74	67	empty
4	303	0.52	0.74	47	empty
5	165	0.47	0.76	24	empty

Interfaces

6 interfaces between chains.

C–D · 1865 Å² buried · 21 hydrogen bonds · protein-protein
H–L · 1858 Å² buried · 18 hydrogen bonds · protein-protein
A–L · 833 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 833 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 442 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 2 modified (disulfide, cyclization).

Compared structures

3ZKM · BACE2 Fab complex · the same entry in another collection · chain L against L, 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 0.96

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 3ZKM · PDBe 3ZKM · UniProt Q9Y5Z0

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