3u8m

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3920 (1-(6-bromopyridin-3-yl)-1,4-diazepane)

Method: X-RAY DIFFRACTION

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

Acetylcholine-binding protein

Lymnaea stagnalis

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 5	1-(6-bromopyridin-3-yl)-1,4-diazepane × 5 SULFATE ION × 6 water × 5	与蛋白数一致
2	蛋白同源多聚体	同源多聚体	蛋白 5	1-(6-bromopyridin-3-yl)-1,4-diazepane × 5 SULFATE ION × 5 water × 5	与蛋白数一致
3	蛋白同源多聚体	同源多聚体	蛋白 5	1-(6-bromopyridin-3-yl)-1,4-diazepane × 5 SULFATE ION × 4 water × 5	与蛋白数一致
4	蛋白同源多聚体	同源多聚体	蛋白 5	1-(6-bromopyridin-3-yl)-1,4-diazepane × 5 SULFATE ION × 2 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	ACHP_LYMST
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–210； UniProt 20–229 作者链 B； PDB构建体 1–210； UniProt 20–229 作者链 C； PDB构建体 1–210； UniProt 20–229 作者链 D； PDB构建体 1–210； UniProt 20–229 作者链 E； PDB构建体 1–210； UniProt 20–229 作者链 F； PDB构建体 1–210； UniProt 20–229 作者链 G； PDB构建体 1–210； UniProt 20–229 作者链 H； PDB构建体 1–210； UniProt 20–229 作者链 I； PDB构建体 1–210； UniProt 20–229 作者链 J； PDB构建体 1–210； UniProt 20–229 作者链 K； PDB构建体 1–210； UniProt 20–229 作者链 L； PDB构建体 1–210； UniProt 20–229 作者链 M； PDB构建体 1–210； UniProt 20–229 作者链 N； PDB构建体 1–210； UniProt 20–229 作者链 O； PDB构建体 1–210； UniProt 20–229 作者链 P； PDB构建体 1–210； UniProt 20–229 作者链 Q； PDB构建体 1–210； UniProt 20–229 作者链 R； PDB构建体 1–210； UniProt 20–229 作者链 S； PDB构建体 1–210； UniProt 20–229 作者链 T； PDB构建体 1–210； UniProt 20–229

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	3u8m
沉积日期 deposition_date	2011-10-17
结构标题 title	Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3920 (1-(6-bromopyridin-3-yl)-1,4-diazepane)
关键词 keywords	;Lymnaea stagnalis, agonist, Ligand-bindig domain, Acetylcholine, Acetylcholine-binding protein, Acetylcholine-binding protein-agonist complex ;; Acetylcholine-binding protein/agonist
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。

3u8m__assembly_1__model_1

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

下载该曲线 .dat

3u8m__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

3u8m__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	31.29 Å
Rg（电子密度）	29.53 Å
总 Rg	30.41 Å
原子数	8095
残基数	1000
排除体积	142390 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	`3u8m__assembly_1__model_1`	pentameric （5）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`3u8m__assembly_2__model_1`	pentameric （5）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
3	1	`3u8m__assembly_3__model_1`	pentameric （5）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
4	1	`3u8m__assembly_4__model_1`	pentameric （5）	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 (4)

实体 1 Entity 1 polymer

描述 description	Acetylcholine-binding protein
分子量 formula_weight	23862.5 kDa
来源方法 src_method	man
拷贝数 entity_count	20

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,I,J,K,L,M,N,O,P,Q,R,S,T
原子数 atom_count	32783

LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSEIL

来源 Source

来源生物 organism	Lymnaea stagnalis
通用名 common_name	Great pond snail
NCBI 分类编号 ncbi_taxonomy_id	6523
宿主生物 host_organism	Spodoptera frugiperda

实体 2 Entity 2 non-polymer

描述 description	1-(6-bromopyridin-3-yl)-1,4-diazepane
分子量 formula_weight	256.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	20

实体 3 Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	17

实体 4 Entity 4 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	328

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6. 折叠分类 (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

结构域编号 domain_id	d3u8ma_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8md_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8me_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mf_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mg_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mh_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mi_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mj_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mk_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8ml_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mm_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mn_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mo_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mp_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mq_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mr_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8ms_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

结构域编号 domain_id	d3u8mt_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamily	b.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family family	b.96.1.1 — Nicotinic receptor ligand binding domain-like

CATH v4.4 (20 domains)

结构域编号 domain_id	3u8mA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mE00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mF00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mH00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mI00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mJ00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mK00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mL00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mM00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mN00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mO00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mP00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mQ00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mR00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mS00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

结构域编号 domain_id	3u8mT00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

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晶胞边长 a length_a	233.057 Å
晶胞边长 b length_b	268.453 Å
晶胞边长 c length_c	73.259 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	80

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	30.010 Å
R 因子 r_factor	0.2200
R_work r_work	0.2190
R_free r_free	0.2750

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3920 (1-(6-bromopyridin-3-yl)-1,4-diazepane)

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

Acetylcholine-binding protein

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

3u8m__assembly_1__model_1

3u8m__assembly_1__model_1 | I(q)

3u8m__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 (4)

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 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. 引用文献 (1)

Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in complex with NS3920 (1-(6-bromopyridin-3-yl)-1,4-diazepane)

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

Acetylcholine-binding protein

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

3u8m__assembly_1__model_1

3u8m__assembly_1__model_1 | I(q)

3u8m__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 (4)

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 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

CATH v4.4 (20 domains)

7. 引用文献 (1)