SAXSdb — 3tz2

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

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	4-PHENYL-BUTANOIC ACID × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCKD_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–412； UniProt 1–412

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	3tz2
Deposition date deposition_date	2011-09-26
Structure title title	Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/phenylbutyrate complex
Keywords keywords	;GHKL protein kinase, Allosteric kinase inhibitor, Branched-chain alpha-ketoacid, Branched-chain amino acids, Maple syrup urine disease, Diabetes and obesity, Bergerat nucleotide-binding fold, Protein kinase, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
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.

3tz2__assembly_1__model_1

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

Download this curve (.dat)

3tz2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3tz2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.01 Å
Rg (electron density)	30.39 Å
Total Rg	30.88 Å
Atom count	4884
Residues	602
Excluded volume	87443 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3tz2__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 (2)

Entity 1 Entity 1 polymer

Description description	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
Molecular weight formula_weight	47374.2 kDa
EC 编号 ec_number	2.7.11.4
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	2459

MILTSVLGSGPRSGSSLWPLLGSSLSLRVRSTSATDTHHVELARERSKTVTSFYNQSAIDVVAEKPSVRLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGFGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHIDGREESFRIHHHHHH

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	4-PHENYL-BUTANOIC ACID
Molecular weight formula_weight	164.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3tz2a1
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.29.5.0 — automated matches

Domain ID domain_id	d3tz2a2
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

CATH v4.4 (2 domains)

Domain ID domain_id	3tz2A01
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	3tz2A02
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

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Unit-cell length a length_a	128.201 Å
Unit-cell length b length_b	128.201 Å
Unit-cell length c length_c	72.111 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 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	38.380 Å
R factor r_factor	0.2040
R_work r_work	0.1990
R_free r_free	0.2420

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/phenylbutyrate complex

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

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, 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

3tz2__assembly_1__model_1

3tz2__assembly_1__model_1 | I(q)

3tz2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/phenylbutyrate complex

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

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, 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

3tz2__assembly_1__model_1

3tz2__assembly_1__model_1 | I(q)

3tz2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)