1rx0

Crystal structure of isobutyryl-CoA dehydrogenase complexed with substrate/ligand.

Method: X-RAY DIFFRACTION

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

Acyl-CoA dehydrogenase family member 8, 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 4	1,2-ETHANEDIOL × 11 FLAVIN-ADENINE DINUCLEOTIDE × 4 ACETIC ACID × 7 METHACRYLYL-COENZYME A × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACAD8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–393； UniProt 24–415 Author chain B； PDBConstruct 2–393； UniProt 24–415 Author chain C； PDBConstruct 2–393； UniProt 24–415 Author chain D； PDBConstruct 2–393； UniProt 24–415

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	1rx0
Deposition date deposition_date	2003-12-18
Structure title title	Crystal structure of isobutyryl-CoA dehydrogenase complexed with substrate/ligand.
Keywords keywords	flavoprotein, dehydrogenase, coenzyme A, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

1rx0__assembly_1__model_1

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

Download this curve (.dat)

1rx0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rx0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.60 Å
Rg (electron density)	33.95 Å
Total Rg	34.37 Å
Atom count	12047
Residues	1535
Excluded volume	213250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rx0__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Acyl-CoA dehydrogenase family member 8, mitochondrial
Molecular weight formula_weight	42746.8 kDa
EC 编号 ec_number	1.3.99.-
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	13784

MVQTGHRSLTSCIDPSMGLNEEQKEFQKVAFDFAAREMAPNMAEWDQKELFPVDVMRKAAQLGFGGVYIQTDVGGSGLSRLDTSVIFEALATGCTSTTAYISIHNMCAWMIDSFGNEEQRHKFCPPLCTMEKFASYCLTEPGSGSDAASLLTSAKKQGDHYILNGSKAFISGAGESDIYVVMCRTGGPGPKGISCIVVEKGTPGLSFGKKEKKVGWNSQPTRAVIFEDCAVPVANRIGSEGQGFLIAVRGLNGGRINIASCSLGAAHASVILTRDHLNVRKQFGEPLASNQYLQFTLADMATRLVAARLMVRNAAVALQEERKDAVALCSMAKLFATDECFAICNQALQMHGGYGYLKDYAVQQYVRDSRVHQILEGSNEVMRILISRSLLQE

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 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	METHACRYLYL-COENZYME A
Molecular weight formula_weight	835.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1472

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1rx0a1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1rx0a2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family family	e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains

Domain ID domain_id	d1rx0b1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1rx0b2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family family	e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains

Domain ID domain_id	d1rx0c1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1rx0c2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family family	e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains

Domain ID domain_id	d1rx0d1
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family family	a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1rx0d2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family family	e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains

CATH v4.4 (12 domains)

Domain ID domain_id	1rx0A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

Domain ID domain_id	1rx0A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

Domain ID domain_id	1rx0A03
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	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	1rx0B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

Domain ID domain_id	1rx0B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

Domain ID domain_id	1rx0B03
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	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	1rx0C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

Domain ID domain_id	1rx0C02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

Domain ID domain_id	1rx0C03
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	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

Domain ID domain_id	1rx0D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

Domain ID domain_id	1rx0D02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

Domain ID domain_id	1rx0D03
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	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

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Unit-cell length a length_a	97.204 Å
Unit-cell length b length_b	134.343 Å
Unit-cell length c length_c	189.641 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	16

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

Resolution resolution	1.770 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1790
R_work r_work	0.1790
R_free r_free	0.1920

Crystal structure of isobutyryl-CoA dehydrogenase complexed with substrate/ligand.

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

Acyl-CoA dehydrogenase family member 8, 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

1rx0__assembly_1__model_1

1rx0__assembly_1__model_1 | I(q)

1rx0__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of isobutyryl-CoA dehydrogenase complexed with substrate/ligand.

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

Acyl-CoA dehydrogenase family member 8, 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

1rx0__assembly_1__model_1

1rx0__assembly_1__model_1 | I(q)

1rx0__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)