7EI0

Crystal structure of falcipain 2 from 3D7 strain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 

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This is version 1.2 of the entry. See complete history


Literature

New insights of falcipain 2 structure from Plasmodium falciparum 3D7 strain.

Chakraborty, S.Alam, B.Biswas, S.

(2022) Biochem Biophys Res Commun 590: 145-151

  • DOI: https://doi.org/10.1016/j.bbrc.2021.12.080
  • Primary Citation of Related Structures:  
    6JW9, 7EI0

  • PubMed Abstract: 

    Malaria identifies as a tropical hallmark, conforming to the burgeoning notion of escalating drug resistance among virulent strains, with the burdensome Plasmodium falciparum under its wing. The cysteine protease Falcipain-2 (FP2) is released in the parasite's food vacuole in the trophozoite stage and contributes to disease progression through its hemoglobinase activity. In the present study, we have determined the crystal structure of FP2 from a drug resistant P. falciparum 3D7 strain. FP2-3D7 sequence has detected four amino acid variants, R12K, E14 N, P100T and G102D, in the mature domain of the protease, when compared with other reported structures. FP2-3D7 protease has been crystallized in the presence of two inhibitors E-64 and Iodoacetamide, which diffracted up to 3.5 Å and 3.4 Å respectively. Structural analyses of the mature domain helped unveil two solvent-exposed pockets with bound ligands where one is structurally homologous to the allosteric binding site of human Cathepsin-K and thus, could be exploited for designing allosteric modifiers of FP2. The structure has also revealed (poly)ethylene glycol molecules along the catalytic cleft, providing interesting insights for exploring FP2 as a chemotherapeutic target and for PEGylation in drug delivery. The side-chains of P2 and P3 residues of E-64 also adopt different rotamer conformations, compared with previously reported structure, emphasizing strain-specific multiple binding-modes of active-site targeted inhibitors. Docking studies, along with normal mode analyses, highlight the mode of hemoglobin binding and the active/inactive switch in hemoglobinase activity, conjecturing the formation of a stable dimeric state with a symmetry related copy in crystal packing.


  • Organizational Affiliation

    Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, 700064, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine proteinase falcipain 2a
A, B
241Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1115700
EC: 3.4.22
UniProt
Find proteins for Q8I6U4 (Plasmodium falciparum (isolate 3D7))
Explore Q8I6U4 
Go to UniProtKB:  Q8I6U4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I6U4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
L [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
A, B
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.55α = 90
b = 115.55β = 90
c = 240.891γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-10-19
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description