3d6b

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

Method: X-RAY DIFFRACTION

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Glutaryl-CoA dehydrogenase

Burkholderia pseudomallei

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白同源多聚体	同源多聚体	蛋白 4	methyl thiophene-2-carboxylate × 1 water × 4	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	Q3JP94_BURP1
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–395； UniProt 1–395 作者链 B； PDB构建体 1–395； UniProt 1–395 作者链 C； PDB构建体 1–395； UniProt 1–395 作者链 D； PDB构建体 1–395； UniProt 1–395

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3d6b
沉积日期 deposition_date	2008-05-19
结构标题 title	2.2 A crystal structure of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei
关键词 keywords	;BURKHOLDERIA, PSEUDOMALLEI, GLUTARYL-COA, DEHYDROGENASE, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, SSGCID, FAD, Flavoprotein, Oxidoreductase ;; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

3d6b__assembly_1__model_1

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

下载该曲线 .dat

3d6b__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

3d6b__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	35.78 Å
Rg（电子密度）	35.17 Å
总 Rg	35.54 Å
原子数	11445
残基数	1488
排除体积	204040 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`3d6b__assembly_1__model_1`	tetrameric （4）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	Glutaryl-CoA dehydrogenase
分子量 formula_weight	43169.2 kDa
EC 编号 ec_number	1.3.99.7
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	11945

MAAATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDIHALILGRAQTGIQAFF

来源 Source

来源生物 organism	Burkholderia pseudomallei
NCBI 分类编号 ncbi_taxonomy_id	320372
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	methyl thiophene-2-carboxylate
分子量 formula_weight	142.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	500

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d3d6ba1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
超家族 Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
家族 Family family	e.6.1.0 — automated matches

结构域编号 domain_id	d3d6ba2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.29 — Bromodomain-like
超家族 Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
家族 Family family	a.29.3.0 — automated matches

结构域编号 domain_id	d3d6bb1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
超家族 Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
家族 Family family	e.6.1.0 — automated matches

结构域编号 domain_id	d3d6bb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.29 — Bromodomain-like
超家族 Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
家族 Family family	a.29.3.0 — automated matches

结构域编号 domain_id	d3d6bc1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
超家族 Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
家族 Family family	e.6.1.0 — automated matches

结构域编号 domain_id	d3d6bc2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.29 — Bromodomain-like
超家族 Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
家族 Family family	a.29.3.0 — automated matches

结构域编号 domain_id	d3d6bd1
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.6 — Acyl-CoA dehydrogenase NM domain-like
超家族 Superfamily superfamily	e.6.1 — Acyl-CoA dehydrogenase NM domain-like
家族 Family family	e.6.1.0 — automated matches

结构域编号 domain_id	d3d6bd2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.29 — Bromodomain-like
超家族 Superfamily superfamily	a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
家族 Family family	a.29.3.0 — automated matches

CATH v4.4 (12 domains)

结构域编号 domain_id	3d6bA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

结构域编号 domain_id	3d6bA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

结构域编号 domain_id	3d6bA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

结构域编号 domain_id	3d6bB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

结构域编号 domain_id	3d6bB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

结构域编号 domain_id	3d6bB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

结构域编号 domain_id	3d6bC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

结构域编号 domain_id	3d6bC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

结构域编号 domain_id	3d6bC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

结构域编号 domain_id	3d6bD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain

结构域编号 domain_id	3d6bD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2

结构域编号 domain_id	3d6bD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3

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晶胞边长 a length_a	98.503 Å
晶胞边长 b length_b	107.472 Å
晶胞边长 c length_c	144.313 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.210 Å
最低分辨率 resolution_low	47.190 Å
R 因子 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. 蛋白身份与相关结构 Protein Identity & Related Structures

Glutaryl-CoA dehydrogenase

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 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. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 water

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

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

1. 蛋白身份与相关结构 Protein Identity & Related Structures

Glutaryl-CoA dehydrogenase

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 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. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 non-polymer

实体 3 Entity 3 water

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)