SAXSdb — 6lio

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

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial

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	GLYCEROL × 3 SULFATE ION × 4 ;4-[[[5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-4-[4-(1-methylsulfonylpiperidin-4-yl)oxyphenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]cyclohexane-1-carboxylic acid ; × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 31–411； UniProt 6–386 Author chain B； PDBConstruct 31–411； UniProt 6–386

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	6lio
Deposition date deposition_date	2019-12-12
Structure title title	Crystal structure of human PDK2 complexed with GM67520
Keywords keywords	mitochondria, kinase, inhibitor, 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.

6lio__assembly_1__model_1

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

Download this curve (.dat)

6lio__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6lio__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.56 Å
Rg (electron density)	29.68 Å
Total Rg	30.32 Å
Atom count	5895
Residues	725
Excluded volume	105250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6lio__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Molecular weight formula_weight	46335.7 kDa
EC 编号 ec_number	2.7.11.2
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	6397

MAGSHHHHHHGMASMTGGQQMGRSGDDDDKALLKNASLAGAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRHYQTIQ

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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	;4-[[[5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-4-[4-(1-methylsulfonylpiperidin-4-yl)oxyphenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]cyclohexane-1-carboxylic acid ;
Molecular weight formula_weight	648.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	451

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d6lioa1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.5 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Family Family family	a.29.5.1 — alpha-ketoacid dehydrogenase kinase, N-terminal domain

Domain ID domain_id	d6lioa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.4 — alpha-ketoacid dehydrogenase kinase, C-terminal domain

Domain ID domain_id	d6liob1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.5 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Family Family family	a.29.5.1 — alpha-ketoacid dehydrogenase kinase, N-terminal domain

Domain ID domain_id	d6liob2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.4 — alpha-ketoacid dehydrogenase kinase, C-terminal domain

Domain ID domain_id	d6liob3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	56.949 Å
Unit-cell length b length_b	95.122 Å
Unit-cell length c length_c	162.503 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	36.530 Å
R factor r_factor	0.2360
R_work r_work	0.2343
R_free r_free	0.2688

Crystal structure of human PDK2 complexed with GM67520

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

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial

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

6lio__assembly_1__model_1

6lio__assembly_1__model_1 | I(q)

6lio__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

7. Citations (1)

Crystal structure of human PDK2 complexed with GM67520

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

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial

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

6lio__assembly_1__model_1

6lio__assembly_1__model_1 | I(q)

6lio__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

7. Citations (1)