1r8y

Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form)

Method: X-RAY DIFFRACTION

▼

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

glycine N-methyltransferase

Mus musculus

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	BETA-MERCAPTOETHANOL × 6 water × 2	与蛋白数一致
2	蛋白同源多聚体	同源多聚体	蛋白 4	BETA-MERCAPTOETHANOL × 4 water × 3	与蛋白数一致
3	蛋白同源多聚体	同源多聚体	蛋白 8	BETA-MERCAPTOETHANOL × 10 water × 5	与蛋白数一致
4	蛋白同源多聚体	同源多聚体	蛋白 8	BETA-MERCAPTOETHANOL × 10 water × 5	与蛋白数一致
5	蛋白同源多聚体	同源多聚体	蛋白 8	BETA-MERCAPTOETHANOL × 10 water × 5	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	GNMT_MOUSE
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–292； UniProt 2–293 作者链 B； PDB构建体 1–292； UniProt 2–293 作者链 C； PDB构建体 1–292； UniProt 2–293 作者链 D； PDB构建体 1–292； UniProt 2–293 作者链 E； PDB构建体 1–292； UniProt 2–293 作者链 F； PDB构建体 1–292； UniProt 2–293 作者链 G； PDB构建体 1–292； UniProt 2–293 作者链 H； PDB构建体 1–292； UniProt 2–293

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。

▼

2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1r8y
沉积日期 deposition_date	2003-10-28
结构标题 title	Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form)
关键词 keywords	Glycine N-Methyltransferase, TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

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。

1r8y__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

1r8y__assembly_3__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

1r8y__assembly_3__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	53.73 Å
Rg（电子密度）	54.01 Å
总 Rg	54.00 Å
原子数	17592
残基数	2265
排除体积	311530 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	`1r8y__assembly_1__model_1`	tetrameric （4）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`1r8y__assembly_2__model_1`	tetrameric （4）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
3	1	`1r8y__assembly_3__model_1`	octameric （8）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
4	1	`1r8y__assembly_4__model_1`	octameric （8）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
5	1	`1r8y__assembly_5__model_1`	octameric （8）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

▶

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

▶

5. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	glycine N-methyltransferase
分子量 formula_weight	32587.0 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	17606

VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGTGRDGSPGFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

实体 2 Entity 2 non-polymer

描述 description	BETA-MERCAPTOETHANOL
分子量 formula_weight	78.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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	14

▼

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1r8ya_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.5 — Glycine N-methyltransferase

结构域编号 domain_id	d1r8yb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.5 — Glycine N-methyltransferase

结构域编号 domain_id	d1r8yc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.5 — Glycine N-methyltransferase

结构域编号 domain_id	d1r8yd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.5 — Glycine N-methyltransferase

结构域编号 domain_id	d1r8ye_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.5 — Glycine N-methyltransferase

结构域编号 domain_id	d1r8yf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.5 — Glycine N-methyltransferase

结构域编号 domain_id	d1r8yg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.5 — Glycine N-methyltransferase

结构域编号 domain_id	d1r8yh_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family family	c.66.1.5 — Glycine N-methyltransferase

CATH v4.4 (16 domains)

结构域编号 domain_id	1r8yA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

结构域编号 domain_id	1r8yA02
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	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1r8yB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

结构域编号 domain_id	1r8yB02
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	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1r8yC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

结构域编号 domain_id	1r8yC02
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	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1r8yD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

结构域编号 domain_id	1r8yD02
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	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1r8yE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

结构域编号 domain_id	1r8yE02
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	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1r8yF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

结构域编号 domain_id	1r8yF02
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	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1r8yG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

结构域编号 domain_id	1r8yG02
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	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	1r8yH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

结构域编号 domain_id	1r8yH02
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	150 — Vaccinia Virus protein VP39

▶

晶胞边长 a length_a	107.980 Å
晶胞边长 b length_b	108.300 Å
晶胞边长 c length_c	119.010 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.71 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	3.000 Å
最低分辨率 resolution_low	13.000 Å
R 因子 r_factor	0.2240
R_work r_work	0.2221
R_free r_free	0.2851

Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form)

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

glycine N-methyltransferase

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

1r8y__assembly_3__model_1

1r8y__assembly_3__model_1 | I(q)

1r8y__assembly_3__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) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. 引用文献 (1)

Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form)

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

glycine N-methyltransferase

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

1r8y__assembly_3__model_1

1r8y__assembly_3__model_1 | I(q)

1r8y__assembly_3__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) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. 引用文献 (1)