6nu1

Crystal Structure of Human PKM2 in Complex with L-cysteine

Method: X-RAY DIFFRACTION

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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	CYSTEINE × 4 1,6-di-O-phosphono-beta-D-fructofuranose × 4 MAGNESIUM ION × 4 OXALATE ION × 4 POTASSIUM ION × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CYSTEINE × 2 1,6-di-O-phosphono-beta-D-fructofuranose × 2 MAGNESIUM ION × 2 OXALATE ION × 2 POTASSIUM ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	CYSTEINE × 2 1,6-di-O-phosphono-beta-D-fructofuranose × 2 MAGNESIUM ION × 2 OXALATE ION × 2 POTASSIUM ION × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	CYSTEINE × 2 1,6-di-O-phosphono-beta-D-fructofuranose × 2 MAGNESIUM ION × 2 OXALATE ION × 2 POTASSIUM ION × 1 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	CYSTEINE × 2 1,6-di-O-phosphono-beta-D-fructofuranose × 2 MAGNESIUM ION × 2 OXALATE ION × 2 POTASSIUM ION × 1 water × 2	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 21–551； UniProt 1–531 Author chain B； PDBConstruct 21–551； UniProt 1–531 Author chain C； PDBConstruct 21–551； UniProt 1–531 Author chain D； PDBConstruct 21–551； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6nu1
Deposition date deposition_date	2019-01-30
Structure title title	Crystal Structure of Human PKM2 in Complex with L-cysteine
Keywords keywords	PYRUVATE KINASE M2, CYSTEINE, INHIBITION, GLYCOLYSIS, 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.

6nu1__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6nu1__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nu1__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	30.01 Å
Rg (electron density)	29.33 Å
Total Rg	29.91 Å
Atom count	7114
Residues	968
Excluded volume	126350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nu1__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6nu1__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6nu1__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6nu1__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6nu1__assembly_5__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 (7)

Entity 1 Entity 1 polymer

Description description	Pyruvate kinase PKM
Molecular weight formula_weight	60188.2 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	15092

MGSSHHHHHHSSGLVPRGSHMSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP

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	CYSTEINE
Molecular weight formula_weight	121.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	616

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Unit-cell length a length_a	81.829 Å
Unit-cell length b length_b	155.918 Å
Unit-cell length c length_c	94.136 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.51 °
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	2.250 Å
Low-resolution limit resolution_low	24.700 Å
R factor r_factor	0.1930
R_work r_work	0.1908
R_free r_free	0.2352

Crystal Structure of Human PKM2 in Complex with L-cysteine

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

6nu1__assembly_4__model_1

6nu1__assembly_4__model_1 | I(q)

6nu1__assembly_4__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 (7)

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 water

7. Citations (1)

Crystal Structure of Human PKM2 in Complex with L-cysteine

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

6nu1__assembly_4__model_1

6nu1__assembly_4__model_1 | I(q)

6nu1__assembly_4__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 (7)

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 water

7. Citations (1)