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Crystal structure of bace complex with BMC005

Analyse Crystal structure of bace complex with BMC005 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5QD9
Type: protein
Length: 1,132 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: E6Y
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-secretase 1 (EC 3.4.23.46)	protein	377	15% helix, 41% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	378	16% helix, 39% strand	P56817

Ligands and binding sites

E6Y · (5S,8S,10R)-8-[(1R)-2-{[1-(3-tert-butylphenyl) cyclopropyl]amino}-1-hydroxyethyl]-4,5,10-trimethyl-1-oxa-4,7-diazacyclohexadecane-3,6-dione · ligand · 3 copies · chains A, B, C

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

Pockets

8 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	1026	0.75	0.78	101	E6Y
2	537	0.71	0.80	64	E6Y
3	575	0.71	0.79	69	E6Y
4	109	0.48	0.80	22	empty
5	158	0.45	0.75	22	empty

Interfaces

2 interfaces between chains.

A–C · 1064 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 597 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5QD9 · Crystal structure of BACE complex with BMC005 · 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 5QD9 · PDBe 5QD9 · UniProt P56817

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