9rdf

Liver Pyruvate kinase in complex with a phthalazine-based fluorescent probe IV

Method: X-RAY DIFFRACTION

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

Isoform L-type of Pyruvate kinase PKLR

Homo sapiens

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 × 3 6-[[7-(dimethylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl]-2-(1~{H}-pyrazol-4-ylmethyl)isoquinolin-1-one × 1 OXALATE ION × 2 1,6-di-O-phosphono-beta-D-fructofuranose × 2 DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 5 6-[[7-(dimethylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl]-2-(1~{H}-pyrazol-4-ylmethyl)isoquinolin-1-one × 1 OXALATE ION × 2 1,6-di-O-phosphono-beta-D-fructofuranose × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KPYR_HUMAN
Isoform	P30613-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–545； UniProt 1–543 Author chain B； PDBConstruct 3–545； UniProt 1–543 Author chain C； PDBConstruct 3–545； UniProt 1–543 Author chain D； PDBConstruct 3–545； UniProt 1–543

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	9rdf
Deposition date deposition_date	2025-06-02
Structure title title	Liver Pyruvate kinase in complex with a phthalazine-based fluorescent probe IV
Keywords keywords	Fragment based drug discovery, kinase, Hydrolase; HYDROLASE
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.

9rdf__assembly_1__model_1

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

Download this curve (.dat)

9rdf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9rdf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.75 Å
Rg (electron density)	29.99 Å
Total Rg	30.62 Å
Atom count	7986
Residues	1042
Excluded volume	142150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rdf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9rdf__assembly_2__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	Isoform L-type of Pyruvate kinase PKLR
Molecular weight formula_weight	58708.3 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	17309

GSMEGPAGYLRRASVAQLTQELGTAFFQQQQLPAAMADTFLEHLCLLDIDSEPVAARSTSIIATIGPASRSVERLKEMIKAGMNIARLNFSHGSHEYHAESIANVREAVESFAGSPLSYRPVAIALDTKGPEIRTGILQGGPESEVELVKGSQVLVTVDPAFRTRGNANTVWVDYPNIVRVVPVGGRIYIDDGLISLVVQKIGPEGLVTQVENGGVLGSRKGVNLPGAQVDLPGLSEQDVRDLRFGVEHGVDIVFASFVRKASDVAAVRAALGPEGHGIKIISKIENHEGVKRFDEILEVSDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNLAGKPVVCATQMLESMITKPRPTRAETSDVANAVLDGADCIMLSGETAKGNFPVEAVKMQHAIAREAEAAVYHRQLFEELRRAAPLSRDPTEVTAIGAVEAAFKCCAAAIIVLTTTGRSAQLLSRYRPRAAVIAVTRSAQAARQVHLCRGVFPLLYREPPEAIWADDVDRRVQFGIESGKLRGFLRVGDLVIVVTGWRPGSGYTNIMRVLSIS

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 BL21(DE3)

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	8

Entity 3 Entity 3 non-polymer

Description description	6-[[7-(dimethylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl]-2-(1~{H}-pyrazol-4-ylmethyl)isoquinolin-1-one
Molecular weight formula_weight	450.5 kDa
Source method src_method	syn
Copy count entity_count	2

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	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 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1145

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Unit-cell length a length_a	200.183 Å
Unit-cell length b length_b	97.584 Å
Unit-cell length c length_c	136.398 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.53 °
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	1.620 Å
Low-resolution limit resolution_low	78.650 Å
R factor r_factor	0.2380
R_work r_work	0.2378
R_free r_free	0.2772

Liver Pyruvate kinase in complex with a phthalazine-based fluorescent probe IV

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

Isoform L-type of Pyruvate kinase PKLR

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

9rdf__assembly_1__model_1

9rdf__assembly_1__model_1 | I(q)

9rdf__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 (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)

Liver Pyruvate kinase in complex with a phthalazine-based fluorescent probe IV

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

Isoform L-type of Pyruvate kinase PKLR

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

9rdf__assembly_1__model_1

9rdf__assembly_1__model_1 | I(q)

9rdf__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 (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)