MolNFT v1 · #66611 · protein

Structure of bace (beta secretase) in complex with EV0

3HVG · Beta-secretase 1: “Structure of bace (beta secretase) in complex with EV0”. X-ray diffraction, 1 ligand (EV0), 7 pockets (best druggability 0.75). MolNFT v1 #66611 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3HVG
Type: protein
Length: 1,122 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1
EC: 3.4.23.46
UniProt: P56817
Ligands: EV0
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 1 (EC 3.4.23.46)	protein	379	15% helix, 41% strand	P56817
B	Beta-secretase 1 (EC 3.4.23.46)	protein	370	15% helix, 39% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	373	12% helix, 42% strand	P56817

Ligands and binding sites

EV0 · 2-amino-6-propylpyrimidin-4(3H)-one · ligand · 3 copies · chains A, B
GOL · Glycerol · additive · chains C

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	497	0.75	0.84	77	EV0
2	457	0.73	0.83	61	GOL
3	477	0.66	0.78	57	EV0
4	150	0.58	0.83	21	empty
5	232	0.51	0.76	31	empty

Interfaces

2 interfaces between chains.

A–C · 615 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 595 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3HVG · Structure of bace (beta secretase) in Complex with EV0 · the same entry in another collection · chain A against A, TM-score 1.00
P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · 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 P56817
Elsewhere: RCSB PDB 3HVG · PDBe 3HVG · UniProt P56817

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