4TRY | pdb_00004try

Structure of BACE1 complex with a HEA-type inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4TRY/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-18 Released: 2015-07-29 
• Deposition Author(s): Akaji, K., Teruya, K., Akiyama, T., Sanjho, A., Yamashita, E., Nakagawa, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structure of BACE1 complex with an anti-HMC-type inhibitor

Akaji, K., Teruya, K., Akiyama, T., Sanjho, A., Yamashita, E., Nakagawa, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 131.93 kDa 
• Atom Count: 9,326 
• Modeled Residue Count: 1,175 
• Deposited Residue Count: 1,176 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	388	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLU-ILE-TIH-THC-NVA	D, E, F	4	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TIH	D, E, F	L-PEPTIDE LINKING	C7 H9 N O2 S		ALA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002106	D, E, F	syn-HEA type inhibitor	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.326	α = 90
b = 102.618	β = 103.53
c = 101.287	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
SCALEPACK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	model building
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Akaji, K., Teruya, K., Akiyama, T., Sanjho, A., Yamashita, E., Nakagawa, A.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description