6VYG | pdb_00006vyg

Cryo-EM structure of Plasmodium vivax hexokinase (Closed state)

• PDB DOI: https://doi.org/10.2210/pdb6VYG/pdb
• EM Map EMD-21459: EMDB EMDataResource

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


• Deposited: 2020-02-26 Released: 2020-05-06 
• Deposition Author(s): Srivastava, S.S., Darling, J.E., Suryadi, J., Morris, J.C., Drew, M.E., Subramaniam, S.
• Funding Organization(s): Canada Excellence Research Chair Award

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Plasmodium vivax and human hexokinases share similar active sites but display distinct quaternary architectures

Srivastava, S.S., Darling, J.E., Suryadi, J., Morris, J.C., Drew, M.E., Subramaniam, S.

(2020) IUCrJ 7: 453-461

• DOI: https://doi.org/10.1107/S2052252520002456

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 227.41 kDa 
• Atom Count: 13,616 
• Modeled Residue Count: 1,732 
• Deposited Residue Count: 2,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotransferase	A, B, C, D	505	Plasmodium vivax	Mutation(s): 0  Gene Names: PVC01_110030900, PVP01_1125500, PVT01_110029900 EC: 2.7.1
UniProt
Find proteins for A5K274 (Plasmodium vivax (strain Salvador I)) Explore A5K274  Go to UniProtKB:  A5K274

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Srivastava, S.S., Darling, J.E., Suryadi, J., Morris, J.C., Drew, M.E., Subramaniam, S.

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Funding Organization	Location	Grant Number
Canada Excellence Research Chair Award	Canada	--

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-06-04
  Changes: Data collection