5MXD

BACE-1 IN COMPLEX WITH LIGAND 32397778

• PDB DOI: https://doi.org/10.2210/pdb5MXD/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-23 Released: 2018-02-14 
• Deposition Author(s): Alexander, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.281 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Literature

Human Beta Secretase 1 In Complex With Ligand 32397778

Alexander, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 145.17 kDa 
• Atom Count: 9,015 
• Modelled Residue Count: 1,140 
• Deposited Residue Count: 1,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	432	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE, KIAA1149 EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817 GTEx:  ENSG00000186318

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
III	D [auth A], F [auth B], H [auth C]	~{N},~{N}-dimethyl-2-pyrrolidin-1-yl-quinazolin-4-amine C14 H18 N4 VONNLDQOEHSECV-UHFFFAOYSA-N
CL	E [auth A], G [auth B], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.281 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 232.913	α = 90
b = 100.737	β = 102.03
c = 59.045	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Alexander, R.

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary