7TBD | pdb_00007tbd

Crystal structure of Plasmepsin X from Plasmodium vivax in complex with WM382

• PDB DOI: https://doi.org/10.2210/pdb7TBD/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium vivax
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-12-21 Released: 2022-05-04 
• Deposition Author(s): Hodder, A.N., Christensen, J.B., Scally, S.W., Cowman, A.F.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Basis for drug selectivity of plasmepsin IX and X inhibition in Plasmodium falciparum and vivax.

Hodder, A.N., Christensen, J., Scally, S., Triglia, T., Ngo, A., Birkinshaw, R.W., Bailey, B., Favuzza, P., Dietrich, M.H., Tham, W.H., Czabotar, P.E., Lowes, K., Guo, Z., Murgolo, N., Lera Ruiz, M., McCauley, J.A., Sleebs, B.E., Olsen, D., Cowman, A.F.

(2022) Structure 30: 947

• PubMed: 35460613 
• DOI: https://doi.org/10.1016/j.str.2022.03.018
• Primary Citation Related Structures: 
  7TBB, 7TBC, 7TBD, 7TBE


• PubMed Abstract: 
  

  Plasmepsins IX (PMIX) and X (PMX) are essential aspartyl proteases for Plasmodium spp. egress, invasion, and development. WM4 and WM382 inhibit PMIX and PMX in Plasmodium falciparum and P. vivax. WM4 inhibits PMX, while WM382 is a dual inhibitor of PMIX and PMX. To understand their function, we identified protein substrates. Enzyme kinetic and structural analyses identified interactions responsible for drug specificity. PMIX and PMX have similar substrate specificity; however, there are distinct differences for peptide and protein substrates. Differences in WM4 and WM382 binding for PMIX and PMX map to variations in the S' region and engagement of the active site S3 pocket. Structures of PMX reveal interactions and mechanistic detail of drug binding important for development of clinical candidates against these targets.

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Organizational Affiliation: 
• The Walter and Eliza Hall Institute of Medical Research, Parkville 3052 VIC, Australia; University of Melbourne, Melbourne, 3010 VIC, Australia.
The Walter and Eliza Hall Institute of Medical Research, Parkville 3052 VIC, Australia.
Merck & Co., Inc, 770 Sumneytown Pike, West Point, PA 19486, USA.
The Walter and Eliza Hall Institute of Medical Research, Parkville 3052 VIC, Australia; University of Melbourne, Melbourne, 3010 VIC, Australia. Electronic address: [e-mail].

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.

Macromolecule Content 

• Total Structure Weight: 87.43 kDa 
• Atom Count: 5,782 
• Modeled Residue Count: 702 
• Deposited Residue Count: 758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin X	A, B	379	Plasmodium vivax	Mutation(s): 0  Gene Names: PVC01_010019000, PVP01_0112200, PVT01_010014800 EC: 3.4.23.1
UniProt
Find proteins for A5KAC3 (Plasmodium vivax (strain Salvador I)) Explore A5KAC3  Go to UniProtKB:  A5KAC3
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I0L (Subject of Investigation/LOI)	E [auth A], H [auth B]	(4R)-4-[(2E)-4,4-diethyl-2-imino-6-oxo-1,3-diazinan-1-yl]-N-[(4S)-2,2-dimethyl-3,4-dihydro-2H-1-benzopyran-4-yl]-3,4-dihydro-2H-1-benzopyran-6-carboxamide C29 H36 N4 O4 ZSZSSSHEMYULPX-FCHUYYIVSA-N
GOL	F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.021	α = 90
b = 88.44	β = 90
c = 230.173	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Hodder, A.N., Christensen, J.B., Scally, S.W., Cowman, A.F.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	109662/Z/15/Z, 202749/Z/16/Z

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2022-07-20
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary