10GI | pdb_000010gi

Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Babesia bovis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 
    0.341 (Depositor), 0.340 (DCC) 
  • R-Value Work: 
    0.290 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.293 (Depositor) 

Starting Model: in silico
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Literature

Expression, purification, crystallization and structure solution of glyceraldehyde-3-phosphate dehydrogenase from the babesiosis infective agent Babesia bovis.

Ukrainski, B.Galvao, E.B.Silva, M.Iulek, J.

(2026) Protein Expr Purif 243: 106991-106991

  • DOI: https://doi.org/10.1016/j.pep.2026.106991
  • Primary Citation Related Structures: 
    10GI

  • PubMed Abstract: 

    Babesia bovis is a species of apicomplexan hemoparasitic protozoa that can be transmitted by ticks, causing a global cattle disease. As it depends mainly on the glycolytic pathway for energy production and life cycle maintenance, glycolytic enzymes are possible targets for drug development against Babesia. Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) has been one of such targets, against several parasitic organisms. It performs the reversible oxidative phosphorylation of glyceraldehyde-3-phosphate to 1,3-bisphospho-D-glycerate in the presence of nicotinamide adenine dinucleotide. The protocol for Babesia bovis Glyceraldehyde-3-Phosphate Dehydrogenase (BbGAPDH) expression and purification has been developed to yields of 28 mg of pure protein per liter of culture medium, with a specific activity of 55.5 ± 6.99 U mg -1 after His-tag removal, indicating preservation of enzymatic activity. For crystallization, the His-tag removal proved essential. Crystals diffracted to 3.12 Å resolution in the P3 1 21 space group; NAD + cofactor molecules are observed in their respective sites. Comparisons to the theoretical model indicate a number of side chain conformation differences. These results provide support for future enzyme inhibition assays, in addition to crystallization assays with potential inhibitors.


  • Organizational Affiliation
    • Chemistry Departament, State University of Ponta Grossa, Paraná, Brazil. Electronic address: ukrainskibruna3@gmail.com.

Macromolecule Content 

  • Total Structure Weight: 78.33 kDa 
  • Atom Count: 5,074 
  • Modeled Residue Count: 675 
  • Deposited Residue Count: 716 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase
A, B
358Babesia bovisMutation(s): 0 
Gene Names: BBOV_II002540
EC: 1.2.1.12
UniProt
Find proteins for A7ATE8 (Babesia bovis)
Explore A7ATE8 
Go to UniProtKB:  A7ATE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7ATE8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free:  0.341 (Depositor), 0.340 (DCC) 
  • R-Value Work:  0.290 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.293 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.614α = 90
b = 85.614β = 90
c = 155.063γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentBrazilPBA2025201000175

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-19
    Type: Initial release
  • Version 1.1: 2026-08-26
    Changes: Database references