1vrq

Crystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with Folinic Acid

Method: X-RAY DIFFRACTION
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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Sarcosine oxidase alpha subunit

Corynebacterium sp.

UniProt Q50LF0

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 蛋白异源复合物 异源复合物 蛋白 4 Sarcosine oxidase beta subunit × 1 (Q50LF2) Sarcosine oxidase gamma subunit × 1 (Q50LE9) Sarcosine oxidase delta subunit × 1 (Q50LF1) SULFATE ION × 13 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 N,N-DIMETHYLGLYCINE × 1 ZINC ION × 1 water × 4 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 8 Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase gamma subunit × 2 (Q50LE9) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 8 Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase gamma subunit × 2 (Q50LE9) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 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 Q50LF0_9CORY
Isoform —
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–964; UniProt 2–965

Sarcosine oxidase beta subunit

Corynebacterium sp.

UniProt Q50LF2

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 蛋白异源复合物 异源复合物 蛋白 4 Sarcosine oxidase alpha subunit × 1 (Q50LF0) Sarcosine oxidase gamma subunit × 1 (Q50LE9) Sarcosine oxidase delta subunit × 1 (Q50LF1) SULFATE ION × 13 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 N,N-DIMETHYLGLYCINE × 1 ZINC ION × 1 water × 4 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase gamma subunit × 2 (Q50LE9) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase gamma subunit × 2 (Q50LE9) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 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 Q50LF2_9CORY
Isoform —
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–404; UniProt 2–405

Sarcosine oxidase gamma subunit

Corynebacterium sp.

UniProt Q50LE9

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 蛋白异源复合物 异源复合物 蛋白 4 Sarcosine oxidase alpha subunit × 1 (Q50LF0) Sarcosine oxidase beta subunit × 1 (Q50LF2) Sarcosine oxidase delta subunit × 1 (Q50LF1) SULFATE ION × 13 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 N,N-DIMETHYLGLYCINE × 1 ZINC ION × 1 water × 4 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 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 Q50LE9_9CORY
Isoform —
PDB实体 3
链与序列区间 作者链 C; PDB构建体 1–200; UniProt 6–205

Sarcosine oxidase delta subunit

Corynebacterium sp.

UniProt Q50LF1

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 蛋白异源复合物 异源复合物 蛋白 4 Sarcosine oxidase alpha subunit × 1 (Q50LF0) Sarcosine oxidase beta subunit × 1 (Q50LF2) Sarcosine oxidase gamma subunit × 1 (Q50LE9) SULFATE ION × 13 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 N,N-DIMETHYLGLYCINE × 1 ZINC ION × 1 water × 4 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase gamma subunit × 2 (Q50LE9) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase gamma subunit × 2 (Q50LE9) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 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 Q50LF1_9CORY
Isoform —
PDB实体 4
链与序列区间 作者链 D; PDB构建体 1–99; UniProt 1–99

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_id1vrq
沉积日期 deposition_date2005-04-27
结构标题 titleCrystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with Folinic Acid
关键词 keywordsHeterotetrameric sarcosine oxidase, flavoenzyme, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 methodX-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。

1vrq__assembly_1__model_1

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

下载该曲线 .dat

1vrq__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 个绘图点;横轴和纵轴均采用对数尺度。

1vrq__assembly_1__model_1 | P(r) · Pending

新版 assembly/model P(r) 尚未计算 此处仅保留位置,不展示旧数据 r (Angstrom) P(r)
P(r) 将按相同 assembly/model 分别计算和展示。
Rg(Guinier)36.14 Å
Rg(电子密度)35.47 Å
总 Rg36.01 Å
原子数12739
残基数1651
排除体积224080 ų
最大 q0.500 Å⁻¹
Assembly Model 结构单元 聚集说明 状态 CRYSOL 操作
1 1 1vrq__assembly_1__model_1 tetrameric (4) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
2 1 1vrq__assembly_2__model_1 octameric (8) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
3 1 1vrq__assembly_3__model_1 octameric (8) 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 (12)

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6. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

结构域编号 domain_id1vrqA02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily120 — Probable tRNA modification gtpase trme; domain 1
结构域编号 domain_id1vrqB01
类 Class class3 — Alpha Beta
架构 Architecture architecture50 — 3-Layer(bba) Sandwich
拓扑 Topology topology50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
结构域编号 domain_id1vrqB02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology9 — D-Amino Acid Oxidase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — D-Amino Acid Oxidase, subunit A, domain 2
结构域编号 domain_id1vrqC01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily120 — Probable tRNA modification gtpase trme; domain 1
结构域编号 domain_id1vrqC02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily1520 — Heterotetrameric sarcosine oxidase
结构域编号 domain_id1vrqD00
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology2270 — Folate-binding fold
同源超家族 H-superfamily homologous superfamily10 — Folate-binding superfamily
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7. 引用文献 (1)