8PRY

Crystal structure of Trypanosoma cruzi glycerol kinase

• PDB DOI: https://doi.org/10.2210/pdb8PRY/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-12 Released: 2024-07-24 
• Deposition Author(s): Lipinski, O., Sonani, R.R., Dubin, G.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.238 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Starting Model: in silico

Literature

Crystal structure of Trypanosoma cruzi glycerol kinase in complex with glycerol

Lipinski, O., Sonani, R.R., Dubin, G.

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 233.45 kDa 
• Atom Count: 16,378 
• Modelled Residue Count: 2,046 
• Deposited Residue Count: 2,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerol kinase	A, B, C, D	523	Trypanosoma cruzi	Mutation(s): 0  Gene Names: C4B63_2g784 EC: 2.7.1.30
UniProt
Find proteins for V5BY50 (Trypanosoma cruzi Dm28c) Explore V5BY50  Go to UniProtKB:  V5BY50

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.238 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.779	α = 117.35
b = 89.321	β = 88.99
c = 97.155	γ = 93.68

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Lipinski, O., Sonani, R.R., Dubin, G.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2020/39/B/NZ1/01551

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary