3d6b

2.2 A crystal structure of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei

Method: X-RAY DIFFRACTION

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

Glutaryl-CoA dehydrogenase

Burkholderia pseudomallei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	methyl thiophene-2-carboxylate × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3JP94_BURP1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–395； UniProt 1–395 Author chain B； PDBConstruct 1–395； UniProt 1–395 Author chain C； PDBConstruct 1–395； UniProt 1–395 Author chain D； PDBConstruct 1–395； UniProt 1–395

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	3d6b
Deposition date deposition_date	2008-05-19
Structure title title	2.2 A crystal structure of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei
Keywords keywords	;BURKHOLDERIA, PSEUDOMALLEI, GLUTARYL-COA, DEHYDROGENASE, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, SSGCID, FAD, Flavoprotein, 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.

3d6b__assembly_1__model_1

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

Download this curve (.dat)

3d6b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d6b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.78 Å
Rg (electron density)	35.17 Å
Total Rg	35.54 Å
Atom count	11445
Residues	1488
Excluded volume	204040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d6b__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 (3)

Entity 1 Entity 1 polymer

Description description	Glutaryl-CoA dehydrogenase
Molecular weight formula_weight	43169.2 kDa
EC 编号 ec_number	1.3.99.7
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	11945

MAAATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDIHALILGRAQTGIQAFF

Source Source

Source organism organism	Burkholderia pseudomallei
NCBI taxonomy ID ncbi_taxonomy_id	320372
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	methyl thiophene-2-carboxylate
Molecular weight formula_weight	142.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	500

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3d6ba1
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.6.1.0 — automated matches

Domain ID domain_id	d3d6ba2
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.29.3.0 — automated matches

Domain ID domain_id	d3d6bb1
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.6.1.0 — automated matches

Domain ID domain_id	d3d6bb2
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.29.3.0 — automated matches

Domain ID domain_id	d3d6bc1
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.6.1.0 — automated matches

Domain ID domain_id	d3d6bc2
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.29.3.0 — automated matches

Domain ID domain_id	d3d6bd1
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.6.1.0 — automated matches

Domain ID domain_id	d3d6bd2
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.29.3.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3d6bA01
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	3d6bA02
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	3d6bA03
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	3d6bB01
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	3d6bB02
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	3d6bB03
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	3d6bC01
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	3d6bC02
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	3d6bC03
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	3d6bD01
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	3d6bD02
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	3d6bD03
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	98.503 Å
Unit-cell length b length_b	107.472 Å
Unit-cell length c length_c	144.313 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	2.210 Å
Low-resolution limit resolution_low	47.190 Å
R factor r_factor	0.2120
R_work r_work	0.2090
R_free r_free	0.2610

2.2 A crystal structure of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei

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

Glutaryl-CoA dehydrogenase

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

3d6b__assembly_1__model_1

3d6b__assembly_1__model_1 | I(q)

3d6b__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

2.2 A crystal structure of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei

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

Glutaryl-CoA dehydrogenase

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

3d6b__assembly_1__model_1

3d6b__assembly_1__model_1 | I(q)

3d6b__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)