MolNFT v1 · #131740 · protein

Crystal structure of bace complex with BMC020 hydrolyzed

5QDD · Beta-secretase 1: “Crystal structure of bace complex with BMC020 hydrolyzed”. X-ray diffraction, 1 ligand (E7A), 5 pockets (best druggability 0.80). MolNFT v1 #131740 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5QDD
Type: protein
Length: 1,112 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: E7A
Pockets: 5 · best druggability 0.80

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	369	15% helix, 41% strand	P56817
B	Beta-secretase 1 (EC 3.4.23.46)	protein	371	15% helix, 42% strand	P56817
C	Beta-secretase 1 (EC 3.4.23.46)	protein	372	15% helix, 40% strand	P56817

Ligands and binding sites

E7A · (10R,12S)-12-[(1R)-1,2-dihydroxyethyl]-N,N,10-trimethyl-14-oxo-2-oxa-13-azabicyclo[13.3.1]nonadeca-1(19),15,17-triene-17-carboxamide · ligand · 3 copies · chains A, B, C
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

5 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	1018	0.80	0.81	135	GOL, E7A
2	484	0.71	0.81	66	GOL, E7A
3	330	0.61	0.78	46	empty
4	225	0.53	0.77	48	empty
5	75	0.37	0.77	19	empty

Interfaces

2 interfaces between chains.

A–C · 1061 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 557 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5QDD · Crystal structure of BACE complex with BMC020 hydrolyzed · the same entry in another collection · chain B against B, 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 5QDD · PDBe 5QDD · UniProt P56817

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