3nvw

Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine

Method: X-RAY DIFFRACTION

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

Xanthine dehydrogenase/oxidase

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 6	FE2/S2 (INORGANIC) CLUSTER × 4 FLAVIN-ADENINE DINUCLEOTIDE × 2 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 2 DIOXOTHIOMOLYBDENUM(VI) ION × 2 GUANINE × 2 water × 6	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	XDH_BOVIN
Isoform	—
PDB实体	1, 2, 3
链与序列区间	作者链 A； PDB构建体 1–164； UniProt 2–165 作者链 J； PDB构建体 1–164； UniProt 2–165 作者链 B； PDB构建体 1–334； UniProt 195–528 作者链 K； PDB构建体 1–334； UniProt 195–528 作者链 C； PDB构建体 1–756； UniProt 571–1326 作者链 L； PDB构建体 1–756； UniProt 571–1326

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	3nvw
沉积日期 deposition_date	2010-07-08
结构标题 title	Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine
关键词 keywords	Hydroxylase, Homodimer, Xanthine Oxidase, Guanine, 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。

3nvw__assembly_1__model_1

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

下载该曲线 .dat

3nvw__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

3nvw__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	44.57 Å
Rg（电子密度）	44.81 Å
总 Rg	44.89 Å
原子数	19322
残基数	2468
排除体积	344850 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	`3nvw__assembly_1__model_1`	hexameric （6）	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 (9)

实体 1 Entity 1 polymer

描述 description	Xanthine dehydrogenase/oxidase
分子量 formula_weight	18002.9 kDa
EC 编号 ec_number	1.17.1.4, 1.17.3.2
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,J
原子数 atom_count	21495

TADELVFFVNGKKVVEKNADPETTLLAYLRRKLGLRGTKLGCGEGGCGACTVMLSKYDRLQDKIIHFSANACLAPICTLHHVAVTTVEGIGSTKTRLHPVQERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIEDAFQGNLCRCTGYRPILQGFRTFAK

实体 2 Entity 2 polymer

描述 description	Xanthine dehydrogenase/oxidase
分子量 formula_weight	37431.5 kDa
EC 编号 ec_number	1.17.1.4, 1.17.3.2
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	B,K

LFNPEEFMPLDPTQEPIFPPELLRLKDVPPKQLRFEGERVTWIQASTLKELLDLKAQHPEAKLVVGNTEIGIEMKFKNQLFPMIICPAWIPELNAVEHGPEGISFGAACALSSVEKTLLEAVAKLPTQKTEVFRGVLEQLRWFAGKQVKSVASLGGNIITASPISDLNPVFMASGTKLTIVSRGTRRTVPMDHTFFPSYRKTLLGPEEILLSIEIPYSREDEFFSAFKQASRREDDIAKVTCGMRVLFQPGSMQVKELALCYGGMADRTISALKTTQKQLSKFWNEKLLQDVCAGLAEELSLSPDAPGGMIEFRRTLTLSFFFKFYLTVLKKLG

实体 3 Entity 3 polymer

描述 description	Xanthine dehydrogenase/oxidase
分子量 formula_weight	83095.4 kDa
EC 编号 ec_number	1.17.1.4, 1.17.3.2
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	C,L

DTVGRPLPHLAAAMQASGEAVYCDDIPRYENELFLRLVTSTRAHAKIKSIDVSEAQKVPGFVCFLSADDIPGSNETGLFNDETVFAKDTVTCVGHIIGAVVADTPEHAERAAHVVKVTYEDLPAIITIEDAIKNNSFYGSELKIEKGDLKKGFSEADNVVSGELYIGGQDHFYLETHCTIAIPKGEEGEMELFVSTQNAMKTQSFVAKMLGVPVNRILVRVKRMGGGFGGKETRSTLVSVAVALAAYKTGHPVRCMLDRNEDMLITGGRHPFLARYKVGFMKTGTIVALEVDHYSNAGNSRDLSHSIMERALFHMDNCYKIPNIRGTGRLCKTNLSSNTAFRGFGGPQALFIAENWMSEVAVTCGLPAEEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYARKSEVDKFNKENCWKKRGLCIIPTKFGISFTVPFLNQAGALIHVYTDGSVLVSHGGTEMGQGLHTKMVQVASKALKIPISKIYISETSTNTVPNSSPTAASVSTDIYGQAVYEACQTILKRLEPFKKKNPDGSWEDWVMAAYQDRVSLSTTGFYRTPNLGYSFETNSGNAFHYFTYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIPTEFRVSLLRDCPNKKAIYASKAVGEPPLFLGASVFFAIKDAIRAARAQHTNNNTKELFRLDSPATPEKIRNACVDKFTTLCVTGAPGNCK

实体 4 Entity 4 non-polymer

描述 description	FE2/S2 (INORGANIC) CLUSTER
分子量 formula_weight	175.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 5 Entity 5 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 6 Entity 6 non-polymer

描述 description	PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
分子量 formula_weight	395.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 7 Entity 7 non-polymer

描述 description	DIOXOTHIOMOLYBDENUM(VI) ION
分子量 formula_weight	161.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 8 Entity 8 non-polymer

描述 description	GUANINE
分子量 formula_weight	151.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 9 Entity 9 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	2173

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d3nvwa1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
家族 Family family	d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins

结构域编号 domain_id	d3nvwa2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.56 — CO dehydrogenase ISP C-domain like
超家族 Superfamily superfamily	a.56.1 — CO dehydrogenase ISP C-domain like
家族 Family family	a.56.1.1 — CO dehydrogenase ISP C-domain like

结构域编号 domain_id	d3nvwb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
家族 Family family	d.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like

结构域编号 domain_id	d3nvwb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
家族 Family family	d.87.2.0 — automated matches

结构域编号 domain_id	d3nvwc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamily	d.41.1 — CO dehydrogenase molybdoprotein N-domain-like
家族 Family family	d.41.1.0 — automated matches

结构域编号 domain_id	d3nvwc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.133 — Molybdenum cofactor-binding domain
超家族 Superfamily superfamily	d.133.1 — Molybdenum cofactor-binding domain
家族 Family family	d.133.1.1 — Molybdenum cofactor-binding domain

结构域编号 domain_id	d3nvwj1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
家族 Family family	d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins

结构域编号 domain_id	d3nvwj2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.56 — CO dehydrogenase ISP C-domain like
超家族 Superfamily superfamily	a.56.1 — CO dehydrogenase ISP C-domain like
家族 Family family	a.56.1.1 — CO dehydrogenase ISP C-domain like

结构域编号 domain_id	d3nvwk1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.145 — FAD-binding/transporter-associated domain-like
超家族 Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
家族 Family family	d.145.1.3 — CO dehydrogenase flavoprotein N-terminal domain-like

结构域编号 domain_id	d3nvwk2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
超家族 Superfamily superfamily	d.87.2 — CO dehydrogenase flavoprotein C-terminal domain-like
家族 Family family	d.87.2.0 — automated matches

结构域编号 domain_id	d3nvwl1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamily	d.41.1 — CO dehydrogenase molybdoprotein N-domain-like
家族 Family family	d.41.1.0 — automated matches

结构域编号 domain_id	d3nvwl2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.133 — Molybdenum cofactor-binding domain
超家族 Superfamily superfamily	d.133.1 — Molybdenum cofactor-binding domain
家族 Family family	d.133.1.1 — Molybdenum cofactor-binding domain

CATH v4.4 (20 domains)

结构域编号 domain_id	3nvwA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	30 — Beta-grasp domain

结构域编号 domain_id	3nvwA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	120 — [2Fe-2S]-binding domain

结构域编号 domain_id	3nvwB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

结构域编号 domain_id	3nvwB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	3nvwB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	50 — CO dehydrogenase flavoprotein, C-terminal domain

结构域编号 domain_id	3nvwC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead

结构域编号 domain_id	3nvwC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	3nvwC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	3nvwC04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	3nvwC05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	3nvwJ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	30 — Beta-grasp domain

结构域编号 domain_id	3nvwJ02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily	120 — [2Fe-2S]-binding domain

结构域编号 domain_id	3nvwK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

结构域编号 domain_id	3nvwK02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	3nvwK03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	50 — CO dehydrogenase flavoprotein, C-terminal domain

结构域编号 domain_id	3nvwL01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead

结构域编号 domain_id	3nvwL02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	3nvwL03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	3nvwL04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

结构域编号 domain_id	3nvwL05
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	365 — Aldehyde Oxidoreductase; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

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晶胞边长 a length_a	132.683 Å
晶胞边长 b length_b	73.396 Å
晶胞边长 c length_c	138.113 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.97 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	131.700 Å
R 因子 r_factor	0.1857
R_work r_work	0.1843
R_free r_free	0.2124

Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine

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

Xanthine dehydrogenase/oxidase

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

3nvw__assembly_1__model_1

3nvw__assembly_1__model_1 | I(q)

3nvw__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

5. 实体与聚合物信息 Entities & Polymers (9)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 polymer

聚合物 Polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 non-polymer

实体 7 Entity 7 non-polymer

实体 8 Entity 8 non-polymer

实体 9 Entity 9 water

6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (12 domains)

CATH v4.4 (20 domains)

7. 引用文献 (1)

Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine

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

Xanthine dehydrogenase/oxidase

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

3nvw__assembly_1__model_1

3nvw__assembly_1__model_1 | I(q)

3nvw__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

5. 实体与聚合物信息 Entities & Polymers (9)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 polymer

聚合物 Polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 non-polymer

实体 7 Entity 7 non-polymer

实体 8 Entity 8 non-polymer

实体 9 Entity 9 water

6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (12 domains)

CATH v4.4 (20 domains)

7. 引用文献 (1)