3UQX

Crystal structure of BACE1 with its inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3UQX/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-11-21 Released: 2012-11-21 
• Deposition Author(s): Chen, T.T., Chen, W.Y., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.186 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Flexibility of the Flap in the Active Site of BACE1 as Revealed by Crystal Structures and MD simulations

Xu, Y.C., Chen, W.Y., Chen, T.T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.66 kDa 
• Atom Count: 3,357 
• Modelled Residue Count: 375 
• Deposited Residue Count: 433 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	433	Homo sapiens	Mutation(s): 2  Gene Names: BACE1 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZPZ	B [auth A]	N-[(1R)-1-(4-fluorophenyl)ethyl]-N'-[(2S,3S)-3-hydroxy-4-{4-[(1S)-1-hydroxyethyl]-1H-1,2,3-triazol-1-yl}-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]benzene-1,3-dicarboxamide C32 H37 F N6 O6 S CUYAHRWSXUTTQB-PELBXYKSSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
URE	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N
CL	M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.186 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.549	α = 90
b = 128.28	β = 90
c = 76.386	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Chen, T.T., Chen, W.Y., Xu, Y.C.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary