1FKN | pdb_00001fkn

Structure of Beta-Secretase Complexed with Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1FKN/pdb

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


• Deposited: 2000-08-09 Released: 2000-10-09 
• Deposition Author(s): Hong, L., Koelsch, G., Lin, X., Wu, S., Terzyan, S., Ghosh, A., Zhang, X.C., Tang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor.

Hong, L., Koelsch, G., Lin, X., Wu, S., Terzyan, S., Ghosh, A.K., Zhang, X.C., Tang, J.

(2000) Science 290: 150-153

• PubMed: 11021803 
• DOI: https://doi.org/10.1126/science.290.5489.150
• Primary Citation Related Structures: 
  1FKN


• PubMed Abstract: 
  

  Memapsin 2 (beta-secretase) is a membrane-associated aspartic protease involved in the production of beta-amyloid peptide in Alzheimer's disease and is a major target for drug design. We determined the crystal structure of the protease domain of human memapsin 2 complexed to an eight-residue inhibitor at 1.9 angstrom resolution. The active site of memapsin 2 is more open and less hydrophobic than that of other human aspartic proteases. The subsite locations from S4 to S2' are well defined. A kink of the inhibitor chain at P2' and the change of chain direction of P3' and P4' may be mimicked to provide inhibitor selectivity.

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Organizational Affiliation: 
• Protein Studies Program and Crystallography Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.04 kDa 
• Atom Count: 6,783 
• Modeled Residue Count: 794 
• Deposited Residue Count: 796 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MEMAPSIN 2	A, B	391	Homo sapiens	Mutation(s): 0  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
inhibitor	C, D	7	N/A	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000290	C, D	BETA-SECRETASE INHIBITOR OM99-2	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.652	α = 90
b = 85.853	β = 101.36
c = 109.237	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-10-09 
Deposition Author(s): Hong, L., Koelsch, G., Lin, X., Wu, S., Terzyan, S., Ghosh, A., Zhang, X.C., Tang, J.

Revision History  

• Version 1.0: 2000-10-09
  Type: Initial release
  
• Version 1.1: 2008-01-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-10-16
  Changes: Structure summary