SAXSdb — 1y8o

▼

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

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 2 （P10515） MAGNESIUM ION × 2 POTASSIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 2 DIHYDROLIPOIC ACID × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDK3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–419； UniProt 9–406

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

Homo sapiens

UniProt P10515

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 × 2 （Q15120） MAGNESIUM ION × 2 POTASSIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 2 DIHYDROLIPOIC ACID × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ODP2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 21–128； UniProt 179–286

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	1y8o
Deposition date deposition_date	2004-12-13
Structure title title	Crystal structure of the PDK3-L2 complex
Keywords keywords	pyruvate dehydrogenase kinase 3, lipoyl-bearing domain, protein-protein complex, 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.

1y8o__assembly_1__model_1

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

Download this curve (.dat)

1y8o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y8o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.50 Å
Rg (electron density)	30.55 Å
Total Rg	31.34 Å
Atom count	7662
Residues	942
Excluded volume	137380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y8o__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3
Molecular weight formula_weight	48291.0 kDa
EC 编号 ec_number	2.7.1.99
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3910

GGSHHHHHHGMARLENLYFQGKQPVPKQIERYSRFSPSPLSIKQFLDFGRDNACEKTSYMFLRKELPVRLANTMREVNLLPDNLLNRPSVGLVQSWYMQSFLELLEYENKSPEDPQVLDNFLQVLIKVRNRHNDVVPTMAQGVIEYKEKFGFDPFISTNIQYFLDRFYTNRISFRMLINQHTLLFGGDTNPVHPKHIGSIDPTCNVADVVKDAYETAKMLCEQYYLVAPELEVEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVELYEDRKEGYPAVKTLVTLGKEDLSIKISDLGGGVPLRKIDRLFNYMYSTAPRPSLEPTRAAPLAGFGYGLPISRLYARYFQGDLKLYSMEGVGTDAVIYLKALSSESFERLPVFNKSAWRHYKTTPEADDWSNPSSEPRDASKYKAKQ

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

Entity 2 Entity 2 polymer

Description description	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Molecular weight formula_weight	14192.1 kDa
EC 编号 ec_number	2.3.1.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GGSHHHHHHGMARLENLYFQGSSYPPHMQVLLPALSPTMTMGTVQRWEKKVGEKLSEGDLLAEIETDKATIGFEVQEEGYLAKILVPEGTRDVPLGTPLCIIVEKEADISAFADYRPTEVTDLKPQVP

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

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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	2

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	DIHYDROLIPOIC ACID
Molecular weight formula_weight	208.3 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	67

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1y8oa1
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	d1y8oa3
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	d1y8ob_
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.1 — Single hybrid motif
Family Family family	b.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains

CATH v4.4 (3 domains)

Domain ID domain_id	1y8oA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	20 — Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain

Domain ID domain_id	1y8oA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	1y8oB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

▶

Unit-cell length a length_a	120.752 Å
Unit-cell length b length_b	120.752 Å
Unit-cell length c length_c	239.153 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.480 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2110
R_work r_work	0.2101
R_free r_free	0.2340

Crystal structure of the PDK3-L2 complex

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

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3

State in the Current Structure

Other States of the Same Protein in the Database

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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

1y8o__assembly_1__model_1

1y8o__assembly_1__model_1 | I(q)

1y8o__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 polymer

Polymer Polymer

Source Source

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

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of the PDK3-L2 complex

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

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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

1y8o__assembly_1__model_1

1y8o__assembly_1__model_1 | I(q)

1y8o__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 polymer

Polymer Polymer

Source Source

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

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)