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Crystal structure of bace complex with BMC024

Analyse Crystal structure of bace complex with BMC024 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5QCS
Type: protein
Length: 1,129 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: AXF
Pockets: 12 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-secretase 1 (EC 3.4.23.46)	protein	375	15% helix, 41% strand	P56817
B, C	Beta-secretase 1 (EC 3.4.23.46)	protein	377	15% helix, 40% strand	P56817

Ligands and binding sites

AXF · (2R,4S)-N-butyl-4-hydroxy-2-methyl- 4-((E)-(4as,12r, 15s,17as)-15-methyl -14,17-dioxo-2,3,4,4A,6,9,11,12, 13, 14,15,16,17,17A-tetradecahydro-1H-5 ,10-dithia-1, 13,16-triaza-benzocycl opentadecen-12-yl)-butyramide · ligand · 3 copies · chains A, B, C

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

Pockets

12 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	513	0.74	0.82	71	AXF
2	377	0.67	0.81	43	AXF
3	411	0.67	0.80	47	AXF
4	138	0.50	0.79	22	empty
5	156	0.49	0.78	26	empty

Interfaces

2 interfaces between chains.

A–C · 1034 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 411 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5QCS · Crystal structure of BACE complex with BMC024 · 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 5QCS · PDBe 5QCS · UniProt P56817

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