3GG8

Crystal structure of the Toxoplasma gondii Pyruvate Kinase N terminal truncated

PDB DOI: https://doi.org/10.2210/pdb3GG8/pdb

Classification: TRANSFERASE
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-27 Released: 2009-05-26
Deposition Author(s): Wernimont, A.K., Lew, J., Allali-Hassani, A., Vedadi, M., Bochkarev, A., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hills, T., Schapira, M., Hui, R., Pizarro, J.C., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.265
R-Value Work: 0.206
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The crystal structure of Toxoplasma gondii pyruvate kinase 1.

Bakszt, R., Wernimont, A., Allali-Hassani, A., Mok, M.W., Hills, T., Hui, R., Pizarro, J.C.

(2010) PLoS One 5: e12736-e12736

PubMed: 20856875 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0012736
Primary Citation of Related Structures:
3EOE, 3GG8

PubMed Abstract:
Pyruvate kinase (PK), which catalyzes the final step in glycolysis converting phosphoenolpyruvate to pyruvate, is a central metabolic regulator in most organisms. Consequently PK represents an attractive therapeutic target in cancer and human pathogens, like Apicomplexans. The phylum Aplicomplexa, a group of exclusively parasitic organisms, includes the genera Plasmodium, Cryptosporidium and Toxoplasma, the etiological agents of malaria, cryptosporidiosis and toxoplasmosis respectively. Toxoplasma gondii infection causes a mild illness and is a very common infection affecting nearly one third of the world's population.

Organizational Affiliation

The Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 224 kDa
Atom Count: 14,796
Modelled Residue Count: 1,915
Deposited Residue Count: 2,044
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B, C, D	511	Toxoplasma gondii	Mutation(s): 0 Gene Names: 55m00007, pk EC: 2.7.1.40
UniProt
Find proteins for Q969A2 (Toxoplasma gondii) Explore Q969A2 Go to UniProtKB: Q969A2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q969A2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B]	E [auth A], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.265
R-Value Work: 0.206
R-Value Observed: 0.209
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.023	α = 90
b = 92.311	β = 105.57
c = 112.443	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-05-26

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2016-06-08
Changes: Other
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description