SAXSdb — 3pp7

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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 4	pyrene-1,3,6,8-tetrasulfonic acid × 2 GLYCEROL × 4 POTASSIUM ION × 8 ;8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID ; × 2 water × 4	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 1–498； UniProt 2–499 Author chain B； PDBConstruct 1–498； UniProt 2–499

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	3pp7
Deposition date deposition_date	2010-11-24
Structure title title	Crystal structure of Leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of glycolysis.
Keywords keywords	TIM Barrel, Glycolysis, ADP/ATP binding, Cytosol, symmetric drug, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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.

3pp7__assembly_1__model_1

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

Download this curve (.dat)

3pp7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pp7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.82 Å
Rg (electron density)	43.19 Å
Total Rg	43.32 Å
Atom count	15216
Residues	1972
Excluded volume	270580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pp7__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 (6)

Entity 1 Entity 1 polymer

Description description	Pyruvate kinase
Molecular weight formula_weight	54336.7 kDa
EC 编号 ec_number	2.7.1.40
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8054

SQLAHNLTLSIFDPVANYRAARIICTIGPSTQSVEALKGLIQSGMSVARMNFSHGSHEYHQTTINNVRQAAAELGVNIAIALDTKGPEIRTGQFVGGDAVMERGATCYVTTDPAFADKGTKDKFYIDYQNLSKVVRPGNYIYIDDGILILQVQSHEDEQTLECTVTNSHTISDRRGVNLPGCDVDLPAVSAKDRVDLQFGVEQGVDMIFASFIRSAEQVGDVRKALGPKGRDIMIICKIENHQGVQNIDSIIEESDGIMVARGDLGVEIPAEKVVVAQKILISKCNVAGKPVICATQMLESMTYNPRPTRAEVSDVANAVFNGADCVMLSGETAKGKYPNEVVQYMARICLEAQSALNEYVFFNSIKKLQHIPMSADEAVCSSAVNSVYETKAKAMVVLSNTGRSARLVAKYRPNCPIVCVTTRLQTCRQLNITQGVESVFFDADKLGHDEGKEHRVAAGVEFAKSKGYVQTGDYCVVIHADHKVKGYANQTRILLVE

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	pyrene-1,3,6,8-tetrasulfonic acid
Molecular weight formula_weight	522.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	;8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID ;
Molecular weight formula_weight	1297.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	436

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3pp7A01
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	3pp7A02
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	3pp7A03
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	3pp7B01
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	3pp7B02
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	3pp7B03
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	123.770 Å
Unit-cell length b length_b	129.480 Å
Unit-cell length c length_c	165.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	44.730 Å
R factor r_factor	0.1934
R_work r_work	0.1914
R_free r_free	0.2312

Crystal structure of Leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of glycolysis.

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

3pp7__assembly_1__model_1

3pp7__assembly_1__model_1 | I(q)

3pp7__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of Leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of glycolysis.

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

3pp7__assembly_1__model_1

3pp7__assembly_1__model_1 | I(q)

3pp7__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)