6SSZ

Structure of the Plasmodium falciparum falcipain 2 protease in complex with an (E)-chalcone inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb6SSZ/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-09-09 Released: 2019-12-04 
• Deposition Author(s): Machin, J., Kantsadi, A., Vakonakis, I.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.308 
• R-Value Work: 0.255 
• R-Value Observed: 0.258 

Literature

The complex of Plasmodium falciparum falcipain-2 protease with an (E)-chalcone-based inhibitor highlights a novel, small, molecule-binding site.

Machin, J.M., Kantsadi, A.L., Vakonakis, I.

(2019) Malar J 18: 388-388

• PubMed: 31791339 
• DOI: https://doi.org/10.1186/s12936-019-3043-0
• Primary Citation of Related Structures:  
  6SSZ


• PubMed Abstract: 
  

  Malaria kills over 400,000 people each year and nearly half the world's population live in at-risk areas. Progress against malaria has recently stalled, highlighting the need for developing novel therapeutics. The parasite haemoglobin degradation pathway, active in the blood stage of the disease where malaria symptoms and lethality manifest, is a well-established drug target. A key enzyme in this pathway is the papain-type protease falcipain-2.

---

Organizational Affiliation: 

Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 54.95 kDa 
• Atom Count: 3,837 
• Modelled Residue Count: 480 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine proteinase falcipain 2a	A, B	242	Plasmodium falciparum	Mutation(s): 1  EC: 3.4.22
UniProt
Find proteins for Q8I6U4 (Plasmodium falciparum (isolate 3D7)) Explore Q8I6U4  Go to UniProtKB:  Q8I6U4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JV1 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(~{E})-3-(1,3-benzodioxol-5-yl)-1-(3-nitrophenyl)prop-2-en-1-one C16 H11 N O5 MALGARLLWBWYQV-GQCTYLIASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.308 
• R-Value Work: 0.255 
• R-Value Observed: 0.258 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.431	α = 90
b = 109.431	β = 90
c = 107.254	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-04 
Deposition Author(s): Machin, J., Kantsadi, A., Vakonakis, I.

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description