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New substrate binding pockets for beta-secretase.

Analyse New substrate binding pockets for beta-secretase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XN2
Type: protein
Length: 1,596 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase 1; OM03-4
EC: 3.4.23.46
UniProt: P56817
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-secretase 1 (EC 3.4.23.46)	protein	389	16% helix, 40% strand	P56817
E, F, G, H	OM03-4	protein	10	0% helix, 20% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1060	0.81	0.82	111	empty
2	309	0.74	0.86	54	empty
3	428	0.72	0.83	35	empty
4	199	0.65	0.84	45	empty
5	387	0.64	0.79	46	empty

Interfaces

9 interfaces between chains.

A–E · 1067 Å² buried · 24 hydrogen bonds · protein-protein
B–F · 1028 Å² buried · 22 hydrogen bonds · protein-protein
C–G · 995 Å² buried · 22 hydrogen bonds · protein-protein
D–H · 990 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 825 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 modified (disulfide, nonstandard).

Compared structures

1XN2 · New substrate binding pockets for beta-secretase. · 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 A against A, TM-score 1.00

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 1XN2 · PDBe 1XN2 · UniProt P56817

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