2c3p

CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus

Method: X-RAY DIFFRACTION

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

PYRUVATE-FERREDOXIN OXIDOREDUCTASE

物种未注明

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 2	IRON/SULFUR CLUSTER × 6 ;1-(2-{(2S,4R,5R)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-[(1S)-1-CARBOXY-1-HYDROXYETHYL]-4-METHYL-1,3-THIAZOLIDIN-5-YL}ETHOXY)-1,1,3,3-TETRAHYDROXY-1LAMBDA~5~-DIPHOSPHOX-1-EN-2-IUM 3-OXIDE ; × 2 MAGNESIUM ION × 2 CALCIUM ION × 2 water × 2	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	P94692_DESAF
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–1231； UniProt 2–1232 作者链 B； PDB构建体 1–1231； UniProt 2–1232

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	2c3p
沉积日期 deposition_date	2005-10-11
结构标题 title	CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus
关键词 keywords	;OXIDOREDUCTASE, 4FE-4S, IRON, IRON-SULFUR, IRON-SULFUR CLUSTER, PYRUVATE CATABOLISM, TPP-DEPENDENT ENZYME, METAL-BINDING, ELECTRON TRANSPORT ;; 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。

2c3p__assembly_1__model_1

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

下载该曲线 .dat

2c3p__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

2c3p__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	38.94 Å
Rg（电子密度）	38.51 Å
总 Rg	39.01 Å
原子数	18882
残基数	2462
排除体积	336530 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	`2c3p__assembly_1__model_1`	dimeric （2）	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 (6)

实体 1 Entity 1 polymer

描述 description	PYRUVATE-FERREDOXIN OXIDOREDUCTASE
分子量 formula_weight	133703.9 kDa
EC 编号 ec_number	1.2.7.1
来源方法 src_method	nat
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	19733

GKKMMTTDGNTATAHVAYAMSEVAAIYPITPSSTMGEEADDWAAQGRKNIFGQTLTIREMQSEAGAAGAVHGALAAGALTTTFTASQGLLLMIPNMYKISGELLPGVFHVTARAIAAHALSIFGDHQDIYAARQTGFAMLASSSVQEAHDMALVAHLAAIESNVPFMHFFDGFRTSHEIQKIEVLDYADMASLVNQKALAEFRAKSMNPEHPHVRGTAQNPDIYFQGREAANPYYLKVPGIVAEYMQKVASLTGRSYKLFDYVGAPDAERVIVSMGSSCETIEEVINHLAAKGEKIGLIKVRLYRPFVSEAFFAALPASAKVITVLDRTKEPGAPGDPLYLDVCSAFVERGEAMPKILAGRYGLGSKEFSPAMVKSVYDNMSGAKKNHFTVGIEDDVTGTSLPVDNAFADTTPKGTIQCQFWGLGADGTVGANKQAIKIIGDNTDLFAQGYFSYDSKKSGGITISHLRFGEKPIQSTYLVNRADYVACHNPAYVGIYDILEGIKDGGTFVLNSPWSSLEDMDKHLPSGIKRTIANKKLKFYNIDAVKIATDVGLGGRINMIMQTAFFKLAGVLPFEKAVDLLKKSIHKAYGKKGEKIVKMNTDAVDQAVTSLQEFKYPDSWKDAPAETKAEPMTNEFFKNVVKPILTQQGDKLPVSAFEADGRFPLGTSQFEKRGVAINVPQWVPENCIQCNQCAFVCPHSAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDCMGCGNCADICPPKEKALVMQPLDTQRDAQVPNLEYAARIPVKSEVLPRDSLKGSQFQEPLMEFSGACSGCGETPYVRVITQLFGERMFIANATGCSSIWGASAPSMPYKTNRLGQGPAWGNSLFEDAAEYGFGMNMSMFARRTHLADLAAKALESDASGDVKEALQGWLAGKNDPIKSKEYGDKLKKLLAGQKDGLLGQIAAMSDLYTKKSVWIFGGDGWAYDIGYGGLDHVLASGEDVNVFVMDTEVYSNTGGQSSKATPTGAVAKFAAAGKRTGKKDLARMVMTYGYVYVATVSMGYSKQQFLKVLKEAESFPGPSLVIAYATCINQGLRKGMGKSQDVMNTAVKSGYWPLFRYDPRLAAQGKNPFQLDSKAPDGSVEEFLMAQNRFAVLDRSFPEDAKRLRAQVAHELDVRFKELEHMAATNIFESFAPAGGKADGSVDFGEGAEFCTRDDTPMMARPDSGEACDQNRAGTSEQQGDLSKRTKK

实体 2 Entity 2 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

实体 3 Entity 3 non-polymer

描述 description	;1-(2-{(2S,4R,5R)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-[(1S)-1-CARBOXY-1-HYDROXYETHYL]-4-METHYL-1,3-THIAZOLIDIN-5-YL}ETHOXY)-1,1,3,3-TETRAHYDROXY-1LAMBDA~5~-DIPHOSPHOX-1-EN-2-IUM 3-OXIDE ;
分子量 formula_weight	516.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 4 Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 5 Entity 5 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 6 Entity 6 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	851

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d2c3pa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.8 — PFOR Pyr module

结构域编号 domain_id	d2c3pa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.12 — PFOR PP module

结构域编号 domain_id	d2c3pa3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.48 — TK C-terminal domain-like
超家族 Superfamily superfamily	c.48.1 — TK C-terminal domain-like
家族 Family family	c.48.1.3 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain II

结构域编号 domain_id	d2c3pa4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.64 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
超家族 Superfamily superfamily	c.64.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
家族 Family family	c.64.1.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III

结构域编号 domain_id	d2c3pa5
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
家族 Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

结构域编号 domain_id	d2c3pb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.8 — PFOR Pyr module

结构域编号 domain_id	d2c3pb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.12 — PFOR PP module

结构域编号 domain_id	d2c3pb3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.48 — TK C-terminal domain-like
超家族 Superfamily superfamily	c.48.1 — TK C-terminal domain-like
家族 Family family	c.48.1.3 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain II

结构域编号 domain_id	d2c3pb4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.64 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
超家族 Superfamily superfamily	c.64.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
家族 Family family	c.64.1.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III

结构域编号 domain_id	d2c3pb5
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
家族 Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

CATH v4.4 (14 domains)

结构域编号 domain_id	2c3pA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	2c3pA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	920 —

结构域编号 domain_id	2c3pA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	920 — Pyruvate-ferredoxin Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III

结构域编号 domain_id	2c3pA04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	780 — Pyruvate-ferredoxin Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Pyruvate-flavodoxin oxidoreductase, EKR domain

结构域编号 domain_id	2c3pA05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2c3pA06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	2c3pA07
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	790 — Pyruvate-ferredoxin Oxidoreductase; domain 7
同源超家族 H-superfamily homologous superfamily	10 — Pyruvate-ferredoxin Oxidoreductase; domain 7

结构域编号 domain_id	2c3pB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	2c3pB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	920 —

结构域编号 domain_id	2c3pB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	920 — Pyruvate-ferredoxin Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III

结构域编号 domain_id	2c3pB04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	780 — Pyruvate-ferredoxin Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Pyruvate-flavodoxin oxidoreductase, EKR domain

结构域编号 domain_id	2c3pB05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2c3pB06
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	2c3pB07
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	790 — Pyruvate-ferredoxin Oxidoreductase; domain 7
同源超家族 H-superfamily homologous superfamily	10 — Pyruvate-ferredoxin Oxidoreductase; domain 7

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晶胞边长 a length_a	85.966 Å
晶胞边长 b length_b	145.840 Å
晶胞边长 c length_c	210.822 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	8

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	2.330 Å
最低分辨率 resolution_low	47.370 Å
R 因子 r_factor	0.1710
R_work r_work	0.1710
R_free r_free	0.2230

CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus

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

PYRUVATE-FERREDOXIN OXIDOREDUCTASE

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

2c3p__assembly_1__model_1

2c3p__assembly_1__model_1 | I(q)

2c3p__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 (6)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 non-polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (10 domains)

CATH v4.4 (14 domains)

7. 引用文献 (2)

CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus

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

PYRUVATE-FERREDOXIN OXIDOREDUCTASE

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

2c3p__assembly_1__model_1

2c3p__assembly_1__model_1 | I(q)

2c3p__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 (6)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 non-polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (10 domains)

CATH v4.4 (14 domains)

7. 引用文献 (2)