Research workbench

Crystal structure of bace complex with BMC001

Analyse Crystal structure of bace complex with BMC001 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5QCT
Type: protein
Length: 1,134 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: E4Y, PO4
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).

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

Ligands and binding sites

E4Y · (2R,4S)-N-butyl-4-[(4S,6R)-16-ethoxy-12-ethyl-6-methyl-2,13-dioxo-3,12-diazabicyclo[12.3.1]octadeca-1(18),14, 16-trien-4-yl]-4-hydroxy-2-methylbutanamide · ligand · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · chains 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	748	0.75	0.80	84	E4Y
2	556	0.72	0.80	67	E4Y
3	551	0.71	0.80	67	E4Y
4	148	0.63	0.86	34	empty
5	165	0.46	0.76	23	empty

Interfaces

2 interfaces between chains.

A–C · 1044 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 499 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5QCT · Crystal structure of BACE complex with BMC001 · 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 5QCT · PDBe 5QCT · UniProt P56817

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.