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Crystal structure of beta-secretase complexed with inhibitor OM00-3

Analyse Crystal structure of beta-secretase complexed with inhibitor OM00-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1M4H
Type: protein
Length: 794 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-secretase; Inhibitor OM00-3
EC: 3.4.23.-
UniProt: P56817
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase (EC 3.4.23.-)	protein	391	16% helix, 39% strand	P56817
B	Beta-secretase (EC 3.4.23.-)	protein	389	16% helix, 39% strand	P56817
C, D	Inhibitor OM00-3	protein	7	0% helix, 29% strand	—

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	394	0.70	0.82	58	empty
2	332	0.60	0.78	35	empty
3	64	0.58	0.90	26	empty
4	68	0.32	0.76	16	empty

Interfaces

3 interfaces between chains.

A–C · 846 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 833 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 496 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

1M4H · Crystal Structure of Beta-secretase complexed with Inhibitor OM00-3 · 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 1M4H · PDBe 1M4H · UniProt P56817

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