9M5O | pdb_00009m5o

Plasmodium vivax aspartyl-tRNA synthetase in complex with aspartyl sulfamoyl adenosine (Asp-AMS) Complex

• PDB DOI: https://doi.org/10.2210/pdb9M5O/pdb

• Classification: LIGASE
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-06 Released: 2025-06-04 
• Deposition Author(s): Sharma, V.K., Manickam, Y., Sharma, A., Bagale, S., Pradeepkumar, P.I.
• Funding Organization(s): Department of Science & Technology (DST, India), Indian Council of Medical Research, Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Natural product-mediated reaction hijacking mechanism validates Plasmodium aspartyl-tRNA synthetase as an antimalarial drug target

Ketprasit, N., Tai, C.W., Sharma, V.K., Manickam, Y., Khandokar, Y., Ye, W., Dogovski, C., Hilko, D.H., Morton, C., Braun, A.S.C., Leeming, M., Bagale, S., Pradeepkumar, P.I., Panjikar, S., Poulsen, S.A., Griffin, M.D.W., Sharma, A., Tilley, L., Xie, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 125.28 kDa 
• Atom Count: 9,167 
• Modeled Residue Count: 1,001 
• Deposited Residue Count: 1,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aspartate--tRNA ligase	A, B	536	Plasmodium vivax	Mutation(s): 0  Gene Names: PVC01_020016700, PVW1_020019400 EC: 6.1.1.12
UniProt
Find proteins for A0A1G4H6Y1 (Plasmodium vivax) Explore A0A1G4H6Y1  Go to UniProtKB:  A0A1G4H6Y1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DSZ (Subject of Investigation/LOI)	C [auth A], F [auth B]	5'-O-(L-alpha-aspartylsulfamoyl)adenosine C14 H19 N7 O9 S KMRBRMHHDAUXAY-UFIIOMENSA-N
MG (Subject of Investigation/LOI)	D [auth A], E [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.253	α = 90
b = 140.253	β = 90
c = 267.611	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data scaling
PHASER	phasing
autoPROC	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Sharma, V.K., Manickam, Y., Sharma, A., Bagale, S., Pradeepkumar, P.I.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	CRG/2023/004351
Indian Council of Medical Research	India	CAR-2024-01-000140
Department of Biotechnology (DBT, India)	India	PR32713

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release