9o3b

PKM2 bound to MCTI-566

Method: X-RAY DIFFRACTION

▼

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

Pyruvate kinase PKM

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	1,6-di-O-phosphono-beta-D-fructofuranose × 2 OXALATE ION × 2 1,2-ETHANEDIOL × 3 MAGNESIUM ION × 4 7-[(dimethylamino)methyl]-8-fluoro-5-methyl-3-[(6-methylpyridin-2-yl)methyl]-3,5-dihydro-4H-pyridazino[4,5-b]indol-4-one × 2 PHOSPHATE ION × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	1,6-di-O-phosphono-beta-D-fructofuranose × 2 OXALATE ION × 2 1,2-ETHANEDIOL × 3 MAGNESIUM ION × 4 7-[(dimethylamino)methyl]-8-fluoro-5-methyl-3-[(6-methylpyridin-2-yl)methyl]-3,5-dihydro-4H-pyridazino[4,5-b]indol-4-one × 2 PHOSPHATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KPYM_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–550； UniProt 1–531 Author chain B； PDBConstruct 20–550； UniProt 1–531 Author chain C； PDBConstruct 20–550； UniProt 1–531 Author chain D； PDBConstruct 20–550； UniProt 1–531 Author chain E； PDBConstruct 20–550； UniProt 1–531 Author chain F； PDBConstruct 20–550； UniProt 1–531 Author chain G； PDBConstruct 20–550； UniProt 1–531 Author chain H； PDBConstruct 20–550； UniProt 1–531

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9o3b
Deposition date deposition_date	2025-04-07
Last revision last_revision	2025-08-13
Structure title title	PKM2 bound to MCTI-566
Keywords keywords	activator, pyruvate kinase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

9o3b__assembly_2__model_1

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

Download this curve (.dat)

9o3b__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9o3b__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	40.47 Å
Rg (electron density)	40.16 Å
Total Rg	40.44 Å
Atom count	15499
Residues	2048
Excluded volume	272880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9o3b__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9o3b__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Pyruvate kinase PKM
Molecular weight formula_weight	60050.1 kDa
EC 编号 ec_number	2.7.1.40
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	32262

MGSSHHHHHHSSGLVPRGSMSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,6-di-O-phosphono-beta-D-fructofuranose
Molecular weight formula_weight	340.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	7-[(dimethylamino)methyl]-8-fluoro-5-methyl-3-[(6-methylpyridin-2-yl)methyl]-3,5-dihydro-4H-pyridazino[4,5-b]indol-4-one
Molecular weight formula_weight	379.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1172

▶

Unit-cell length a length_a	80.807 Å
Unit-cell length b length_b	93.855 Å
Unit-cell length c length_c	153.660 Å
Unit-cell angle α angle_alpha	89.73 °
Unit-cell angle β angle_beta	89.68 °
Unit-cell angle γ angle_gamma	75.79 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.416 Å
Low-resolution limit resolution_low	45.490 Å
R factor r_factor	0.1878
R_work r_work	0.1858
R_free r_free	0.2263

PKM2 bound to MCTI-566

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

Pyruvate kinase PKM

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

9o3b__assembly_2__model_1

9o3b__assembly_2__model_1 | I(q)

9o3b__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 (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

7. Citations (1)

PKM2 bound to MCTI-566

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

Pyruvate kinase PKM

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

9o3b__assembly_2__model_1

9o3b__assembly_2__model_1 | I(q)

9o3b__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 (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

7. Citations (1)