1u8v

Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum: Radical catalysis involving a [4Fe-4S] cluster and flavin

Method: X-RAY DIFFRACTION

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

Gamma-aminobutyrate metabolism dehydratase/isomerase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	IRON/SULFUR CLUSTER × 4 FLAVIN-ADENINE DINUCLEOTIDE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDVD_CLOAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–490； UniProt 1–490 Author chain B； PDBConstruct 1–490； UniProt 1–490 Author chain C； PDBConstruct 1–490； UniProt 1–490 Author chain D； PDBConstruct 1–490； UniProt 1–490

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	1u8v
Deposition date deposition_date	2004-08-07
Structure title title	Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum: Radical catalysis involving a [4Fe-4S] cluster and flavin
Keywords keywords	alfa-helixes, beta-strands, LYASE, ISOMERASE; LYASE, ISOMERASE
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.

1u8v__assembly_1__model_1

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

Download this curve (.dat)

1u8v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1u8v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.18 Å
Rg (electron density)	36.62 Å
Total Rg	36.83 Å
Atom count	15488
Residues	1960
Excluded volume	274410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1u8v__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 (4)

Entity 1 Entity 1 polymer

Description description	Gamma-aminobutyrate metabolism dehydratase/isomerase
Molecular weight formula_weight	54572.1 kDa
EC 编号 ec_number	4.2.-.-, 5.3.3.3
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17824

MLMTAEQYIESLRKLNTRVYMFGEKIENWVDHPMIRPSINCVRMTYELAQDPQYADLMTTKSNLIGKTINRFANLHQSTDDLRKKVKMQRLLGQKTASCFQRCVGMDAFNAVFSTTYEIDQKYGTNYHKNFTEYLKYIQENDLIVDGAMTDPKGDRGLAPSAQKDPDLFLRIVEKREDGIVVRGAKAHQTGSINSHEHIIMPTIAMTEADKDYAVSFACPSDADGLFMIYGRQSCDTRKMEEGADIDLGNKQFGGQEALVVFDNVFIPNDRIFLCQEYDFAGMMVERFAGYHRQSYGGCKVGVGDVVIGAAALAADYNGAQKASHVKDKLIEMTHLNETLYCCGIACSAEGYPTAAGNYQIDLLLANVCKQNITRFPYEIVRLAEDIAGGLMVTMPSEADFKSETVVGRDGETIGDFCNKFFAAAPTCTTEERMRVLRFLENICLGASAVGYRTESMHGAGSPQAQRIMIARQGNINAKKELAKAIAGIK

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	4

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2336

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1u8va1
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	d1u8va2
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	d1u8vb1
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	d1u8vb2
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	d1u8vc1
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	d1u8vc2
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	d1u8vd1
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	d1u8vd2
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	1u8vA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3140 — 4-hydroxybutyryl-coa dehydratase, domain 1
Homologous superfamily homologous superfamily	10 — 4-hydroxybutyryl-coa dehydratase, domain 1

Domain ID domain_id	1u8vA02
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	1u8vA03
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	1u8vB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3140 — 4-hydroxybutyryl-coa dehydratase, domain 1
Homologous superfamily homologous superfamily	10 — 4-hydroxybutyryl-coa dehydratase, domain 1

Domain ID domain_id	1u8vB02
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	1u8vB03
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	1u8vC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3140 — 4-hydroxybutyryl-coa dehydratase, domain 1
Homologous superfamily homologous superfamily	10 — 4-hydroxybutyryl-coa dehydratase, domain 1

Domain ID domain_id	1u8vC02
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	1u8vC03
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	1u8vD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3140 — 4-hydroxybutyryl-coa dehydratase, domain 1
Homologous superfamily homologous superfamily	10 — 4-hydroxybutyryl-coa dehydratase, domain 1

Domain ID domain_id	1u8vD02
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	1u8vD03
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	102.300 Å
Unit-cell length b length_b	130.200 Å
Unit-cell length c length_c	175.500 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	1.600 Å
Low-resolution limit resolution_low	58.000 Å
R factor r_factor	0.1650
R_work r_work	0.1630
R_free r_free	0.2120

Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum: Radical catalysis involving a [4Fe-4S] cluster and flavin

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

Gamma-aminobutyrate metabolism dehydratase/isomerase

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

1u8v__assembly_1__model_1

1u8v__assembly_1__model_1 | I(q)

1u8v__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum: Radical catalysis involving a [4Fe-4S] cluster and flavin

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

Gamma-aminobutyrate metabolism dehydratase/isomerase

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

1u8v__assembly_1__model_1

1u8v__assembly_1__model_1 | I(q)

1u8v__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)