3hqo

Crystal structures of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP and Oxalate

Method: X-RAY DIFFRACTION

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

Pyruvate kinase

Leishmania mexicana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 4 POTASSIUM ION × 2 OXALATE ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 4 POTASSIUM ION × 2 OXALATE ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KPYK_LEIME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–499； UniProt 1–499 Author chain B； PDBConstruct 1–499； UniProt 1–499 Author chain C； PDBConstruct 1–499； UniProt 1–499 Author chain K； PDBConstruct 1–499； UniProt 1–499

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	3hqo
Deposition date deposition_date	2009-06-08
Structure title title	Crystal structures of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP and Oxalate
Keywords keywords	TIM BARREL, R-STATE ENZYME, Allosteric enzyme, Glycolysis, Kinase, Magnesium, Metal-binding, Pyruvate, Transferase; 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.

3hqo__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3hqo__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hqo__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	39.08 Å
Rg (electron density)	39.40 Å
Total Rg	39.37 Å
Atom count	7574
Residues	982
Excluded volume	134280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hqo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3hqo__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3hqo__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3hqo__assembly_4__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	Pyruvate kinase
Molecular weight formula_weight	54467.9 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	K,A,B,C
Atom count atom_count	15214

MSQLAHNLTLSIFDPVANYRAARIICTIGPSTQSVEALKGLIQSGMSVARMNFSHGSHEYHQTTINNVRQAAAELGVNIAIALDTKGPEIRTGQFVGGDAVMERGATCYVTTDPAFADKGTKDKFYIDYQNLSKVVRPGNYIYIDDGILILQVQSHEDEQTLECTVTNSHTISDRRGVNLPGCDVDLPAVSAKDRVDLQFGVEQGVDMIFASFIRSAEQVGDVRKALGPKGRDIMIICKIENHQGVQNIDSIIEESDGIMVARGDLGVEIPAEKVVVAQKILISKCNVAGKPVICATQMLESMTYNPRPTRAEVSDVANAVFNGADCVMLSGETAKGKYPNEVVQYMARICLEAQSALNEYVFFNSIKKLQHIPMSADEAVCSSAVNSVYETKAKAMVVLSNTGRSARLVAKYRPNCPIVCVTTRLQTCRQLNITQGVESVFFDADKLGHDEGKEHRVAAGVEFAKSKGYVQTGDYCVVIHADHKVKGYANQTRILLVE

Source Source

Source organism organism	Leishmania mexicana
NCBI taxonomy ID ncbi_taxonomy_id	5665
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	OXALATE ION
Molecular weight formula_weight	88.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3hqoA01
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	3hqoA02
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	3hqoA03
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	3hqoB01
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	3hqoB02
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	3hqoB03
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	3hqoC01
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	3hqoC02
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	3hqoC03
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	3hqoK01
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	3hqoK02
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	3hqoK03
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

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Unit-cell length a length_a	107.516 Å
Unit-cell length b length_b	128.133 Å
Unit-cell length c length_c	204.361 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	41.180 Å
R factor r_factor	0.2524
R_work r_work	0.2505
R_free r_free	0.2895

Crystal structures of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP and Oxalate

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

3hqo__assembly_2__model_1

3hqo__assembly_2__model_1 | I(q)

3hqo__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structures of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP and Oxalate

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

3hqo__assembly_2__model_1

3hqo__assembly_2__model_1 | I(q)

3hqo__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)