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Apo structure of BACE1

Analyse Apo structure of BACE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TPL
Type: protein
Length: 1,118 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: SO4, CL
Pockets: 5 · best druggability 0.70

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	371	13% helix, 41% strand	P56817
B	Beta-secretase 1 (EC 3.4.23.46)	protein	377	13% helix, 40% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	370	15% helix, 41% strand	P56817

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, C
CL · Chloride ion · ion · chains B

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

Pockets

5 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	388	0.70	0.82	56	empty
2	376	0.70	0.82	52	empty
3	421	0.69	0.81	54	empty
4	246	0.57	0.78	38	empty
5	218	0.53	0.77	43	empty

Interfaces

1 interface between chains.

A–B · 461 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3TPL · APO Structure of BACE1 · 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 C 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 3TPL · PDBe 3TPL · UniProt P56817

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