SAXSdb — 3eoe

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pyruvate kinase

Toxoplasma gondii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	GLYCEROL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q969A2_TOXGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–511； UniProt 39–531 Author chain B； PDBConstruct 19–511； UniProt 39–531 Author chain C； PDBConstruct 19–511； UniProt 39–531 Author chain D； PDBConstruct 19–511； UniProt 39–531

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3eoe
Deposition date deposition_date	2008-09-26
Structure title title	Crystal Structure of Pyruvate Kinase from toxoplasma gondii, 55.m00007
Keywords keywords	malaria kinase pyruvate structural genomics, Glycolysis, Magnesium, Metal-binding, Transferase, Structural Genomics Consortium, SGC; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3eoe__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3eoe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3eoe__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.23 Å
Rg (electron density)	42.90 Å
Total Rg	43.06 Å
Atom count	13368
Residues	1812
Excluded volume	239320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3eoe__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Pyruvate kinase
Molecular weight formula_weight	55929.4 kDa
EC 编号 ec_number	2.7.1.40
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14040

MHHHHHHSSGRENLYFQGIRMSQILEPRSEEDWTAHRTRIVCTMGPACWNVDTLVKMIDAGMNVCRLNFSHGDHETHARTVQNIQEAMKQRPEARLAILLDTKGPEIRTGFLKDHKPITLQQGATLKIVTDYNLIGDETTIACSYGALPQSVKPGNTILIADGSLSVKVVEVGSDYVITQAQNTATIGERKNMNLPNVKVQLPVIGEKDKHDILNFGIPMGCNFIAASFVQSADDVRYIRGLLGPRGRHIRIIPKIENVEGLVNFDEILAEADGIMIARGDLGMEIPPEKVFLAQKMMIAKCNVVGKPVITATQMLESMIKNPRPTRAEAADVANAVLDGTDCVMLSGETANGEFPVITVETMARICYEAETCVDYPALYRAMCLAVPPPISTQEAVARAAVETAECVNAAIILALTETGQTARLIAKYRPMQPILALSASESTIKHLQVIRGVTTMQVPSFQGTDHVIRNAIVVAKERELVTEGESIVAVHGMKEEVAGSSNLLKVLTVE

Source Source

Source organism organism	Toxoplasma gondii
NCBI taxonomy ID ncbi_taxonomy_id	5811
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	639

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6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id	3eoeA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	3eoeA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3eoeA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily	10 — PK beta-barrel domain-like

Domain ID domain_id	3eoeB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	3eoeB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3eoeB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily	10 — PK beta-barrel domain-like

Domain ID domain_id	3eoeC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	3eoeC02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3eoeC03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily	10 — PK beta-barrel domain-like

Domain ID domain_id	3eoeD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	3eoeD02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

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Unit-cell length a length_a	98.039 Å
Unit-cell length b length_b	130.684 Å
Unit-cell length c length_c	113.848 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	42.680 Å
R factor r_factor	0.2080
R_work r_work	0.2060
R_free r_free	0.2530

Crystal Structure of Pyruvate Kinase from toxoplasma gondii, 55.m00007

1. Protein Identity and Related Structures Protein Identity & Related Structures

Pyruvate kinase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3eoe__assembly_1__model_1

3eoe__assembly_1__model_1 | I(q)

3eoe__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)

Crystal Structure of Pyruvate Kinase from toxoplasma gondii, 55.m00007

1. Protein Identity and Related Structures Protein Identity & Related Structures

Pyruvate kinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3eoe__assembly_1__model_1

3eoe__assembly_1__model_1 | I(q)

3eoe__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)