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Crystal structure of bace complex with BMC003

Analyse Crystal structure of bace complex with BMC003 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5QD8
Type: protein
Length: 1,135 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: E6V
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 15% 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	381	15% helix, 39% strand	P56817

Ligands and binding sites

E6V · (3S,14R,16S)-16-[(1R)-2-{[(4S)-2,2-dimethyl-6-(propan-2-yl)-3,4-dihydro-2H-1-benzopyran-4-yl]amino}-1-hydroxyethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5-dione · ligand · 3 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	787	0.74	0.79	83	E6V
2	568	0.72	0.80	69	E6V
3	704	0.72	0.79	82	E6V
4	148	0.56	0.82	30	empty
5	172	0.56	0.81	27	empty

Interfaces

2 interfaces between chains.

A–C · 1069 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 555 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5QD8 · Crystal structure of BACE complex with BMC003 · 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 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 5QD8 · PDBe 5QD8 · UniProt P56817

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