9C5N | pdb_00009c5n

Trypanosoma cruzi R19T/K20S/C64Y mutant beta-3-HBDH APO structure

• PDB DOI: https://doi.org/10.2210/pdb9C5N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-06-06 Released: 2025-08-27 
• Deposition Author(s): Hashimoto, H., Debler, E.W.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Trypanosoma cruzi D-3-hydroxybutyrate dehydrogenase (HBDH) is NADP-dependent enzyme.

Hashimoto, H., Debler, E.W.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 114.75 kDa 
• Atom Count: 8,615 
• Modeled Residue Count: 1,045 
• Deposited Residue Count: 1,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxybutyrate dehydrogenase	A, B, C, D	270	Trypanosoma cruzi	Mutation(s): 3  Gene Names: C4B63_13g310 EC: 1.1.1.100
UniProt
Find proteins for A0A2V2VPF1 (Trypanosoma cruzi) Explore A0A2V2VPF1  Go to UniProtKB:  A0A2V2VPF1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth C], K [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.53	α = 90
b = 80.27	β = 107.09
c = 122.52	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Hashimoto, H., Debler, E.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI165840

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release