3hqp

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate

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 monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 GLYCEROL × 1 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
13	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
14	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
15	Protein monomer	Monomer	Protein 1	POTASSIUM ION × 2 2,6-di-O-phosphono-beta-D-fructofuranose × 1 GLYCEROL × 1 water × 1	Consistent with protein count
16	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 GLYCEROL × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 GLYCEROL × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 POTASSIUM ION × 2 OXALATE ION × 1 2,6-di-O-phosphono-beta-D-fructofuranose × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 GLYCEROL × 2 water × 1	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 D； PDBConstruct 1–499； UniProt 1–499 Author chain E； PDBConstruct 1–499； UniProt 1–499 Author chain F； PDBConstruct 1–499； UniProt 1–499 Author chain G； PDBConstruct 1–499； UniProt 1–499 Author chain H； PDBConstruct 1–499； UniProt 1–499 Author chain I； PDBConstruct 1–499； UniProt 1–499 Author chain J； PDBConstruct 1–499； UniProt 1–499 Author chain K； PDBConstruct 1–499； UniProt 1–499 Author chain L； PDBConstruct 1–499； UniProt 1–499 Author chain M； PDBConstruct 1–499； UniProt 1–499 Author chain N； PDBConstruct 1–499； UniProt 1–499 Author chain O； PDBConstruct 1–499； UniProt 1–499 Author chain P； 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	3hqp
Deposition date deposition_date	2009-06-08
Structure title title	Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate
Keywords keywords	TIM BARREL, T-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.

3hqp__assembly_16__model_1

Assembly 16 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3hqp__assembly_16__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hqp__assembly_16__model_1 | P(r) · Pending

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

Rg（Guinier）	24.76 Å
Rg (electron density)	24.12 Å
Total Rg	24.78 Å
Atom count	3860
Residues	498
Excluded volume	68430 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hqp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3hqp__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3hqp__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3hqp__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3hqp__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3hqp__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3hqp__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3hqp__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3hqp__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3hqp__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3hqp__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3hqp__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`3hqp__assembly_13__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`3hqp__assembly_14__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
15	1	`3hqp__assembly_15__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
16	1	`3hqp__assembly_16__model_1`	monomeric （1）	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 (8)

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	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	65997

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	30

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	32

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	15

Entity 5 Entity 5 non-polymer

Description description	2,6-di-O-phosphono-beta-D-fructofuranose
Molecular weight formula_weight	340.1 kDa
Source method src_method	man
Copy count entity_count	16

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4100

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6. Fold Classification (SCOP + CATH) 96 domains

SCOP 2.08 (48 domains)

Domain ID domain_id	d3hqpa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpa2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpb2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpc2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpc3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpd2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpd3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpe1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpe2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpe3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpf2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpf3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpg1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpg2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpg3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqph1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqph2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqph3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpi1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpi2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpi3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpj1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpj2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpj3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpk1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpk2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpk3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpl1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpl2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpl3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpm1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpm2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpm3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpn1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpn2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpn3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpo1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpo2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpo3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d3hqpp1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d3hqpp2
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d3hqpp3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

CATH v4.4 (48 domains)

Domain ID domain_id	3hqpA01
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	3hqpA02
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	3hqpA03
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	3hqpB01
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	3hqpB02
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	3hqpB03
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	3hqpC01
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	3hqpC02
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	3hqpC03
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	3hqpD01
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	3hqpD02
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	3hqpD03
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	3hqpE01
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	3hqpE02
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	3hqpE03
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	3hqpF01
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	3hqpF02
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	3hqpF03
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	3hqpG01
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	3hqpG02
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	3hqpG03
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	3hqpH01
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	3hqpH02
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	3hqpH03
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	3hqpI01
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	3hqpI02
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	3hqpI03
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	3hqpJ01
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	3hqpJ02
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	3hqpJ03
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	3hqpK01
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	3hqpK02
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	3hqpK03
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	3hqpL01
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	3hqpL02
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	3hqpL03
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	3hqpM01
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	3hqpM02
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	3hqpM03
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	3hqpN01
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	3hqpN02
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	3hqpN03
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	3hqpO01
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	3hqpO02
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	3hqpO03
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	3hqpP01
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	3hqpP02
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	3hqpP03
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

▶

Unit-cell length a length_a	127.486 Å
Unit-cell length b length_b	151.140 Å
Unit-cell length c length_c	160.319 Å
Unit-cell angle α angle_alpha	89.73 °
Unit-cell angle β angle_beta	80.17 °
Unit-cell angle γ angle_gamma	71.64 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	34.460 Å
R factor r_factor	0.2011
R_work r_work	0.1984
R_free r_free	0.2520

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate

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

3hqp__assembly_16__model_1

3hqp__assembly_16__model_1 | I(q)

3hqp__assembly_16__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 (8)

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

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 96 domains

SCOP 2.08 (48 domains)

CATH v4.4 (48 domains)

7. Citations (1)

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate

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

3hqp__assembly_16__model_1

3hqp__assembly_16__model_1 | I(q)

3hqp__assembly_16__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 (8)

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

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 96 domains

SCOP 2.08 (48 domains)

CATH v4.4 (48 domains)

7. Citations (1)