3wtn

Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid

Method: X-RAY DIFFRACTION Dmax: 131.5 Å Quality: GOOD

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

Acetylcholine-binding protein

Lymnaea stagnalis

UniProt P58154

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白同源多聚体 同源多聚体 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 A; UniProt 21–229 链 B; UniProt 21–229 链 C; UniProt 21–229 链 D; UniProt 21–229 链 E; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 5 CD CADMIUM ION × 35 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
10 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 H; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
11 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 I; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 6 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
12 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 J; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
2 蛋白同源多聚体 同源多聚体 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 F; UniProt 21–229 链 G; UniProt 21–229 链 H; UniProt 21–229 链 I; UniProt 21–229 链 J; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 5 CD CADMIUM ION × 19 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
3 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 A; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 8 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
4 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 B; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 7 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
5 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 C; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 7 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
6 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 D; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 7 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
7 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 E; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 6 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
8 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 F; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262
9 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 G; UniProt 21–229 片段:UNP residues 21-229 N2Y (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine × 1 CD CADMIUM ION × 5 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;293 K;1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K 分辨率 2.09 Å R-free 0.262

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 59 个其他 PDB 条目、111 个 assembly。 打开独立比较页并筛选聚集状态

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 6–214; UniProt 21–229 作者链 B; PDB构建体 6–214; UniProt 21–229 作者链 C; PDB构建体 6–214; UniProt 21–229 作者链 D; PDB构建体 6–214; UniProt 21–229 作者链 E; PDB构建体 6–214; UniProt 21–229 作者链 F; PDB构建体 6–214; UniProt 21–229 作者链 G; PDB构建体 6–214; UniProt 21–229 作者链 H; PDB构建体 6–214; UniProt 21–229 作者链 I; PDB构建体 6–214; UniProt 21–229 作者链 J; PDB构建体 6–214; UniProt 21–229

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。

SAXS 散射曲线 SAXS Profile

SAXS profile for 3wtn

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3wtn
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3wtn
沉积日期 deposition_date2014-04-11
结构标题 titleCrystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid
关键词 keywordsneonicotinoids, nicotinic acetylcholine receptor, imidacloprid, acetylcholine binding, SIGNALING PROTEIN; SIGNALING PROTEIN
实验方法 methodX-RAY DIFFRACTION

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier41.14
回转半径 Rg (电子) rg_electron40.23
零角强度 I(0) i0997456000.00
分子量 molecular_weight242640.0 kDa
排除体积 excluded_volume295050 ų
包络体积 envelope_volume387260 ų
水化壳体积 shell_volume78395 ų
包络直径 envelope_diameter134.7
壳层 Rg shell_rg47.31
包络 Rg envelope_rg38.99
形状 Rg shape_rg40.16
总 Rg total_rg40.80
总原子数 total_atoms16716
残基数 n_residues2080
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax131.5
Rg (实空间) rg_real40.98
Rg 误差 (实空间) rg_real_error0.93
I(0) (实空间) i0_real9.9750e+08
I(0) 误差 (实空间) i0_real_error1.7330e+07
Rg (倒空间) rg_reciprocal41.14
I(0) (倒空间) i0_reciprocal997600000.0000
解质量估计 total_estimate0.8690
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary51.9
偏度 Skewness skewness0.241
峰度 Kurtosis kurtosis-0.300
角度范围 angular_range— – 0.1900 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha143400000.0000
实空间数据点数 n_real_points39
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.885

5. 晶体学与实验 5. Crystallography & Experiment

6. 实体与聚合物信息 Entities & Polymers (5)

7. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

结构域编号 domain_idd3wtna1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtna2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd3wtnb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtnb2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd3wtnc1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtnc2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd3wtnd1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtnd2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd3wtne1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtne2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd3wtnf1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtnf2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd3wtng1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtng2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd3wtnh1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtnh2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd3wtni1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtni2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd3wtnj1
类 Class classb — All beta proteins
折叠类型 Fold foldb.96 — Nicotinic receptor ligand binding domain-like
超家族 Superfamily superfamilyb.96.1 — Nicotinic receptor ligand binding domain-like
家族 Family familyb.96.1.1 — Nicotinic receptor ligand binding domain-like
结构域编号 domain_idd3wtnj2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags

CATH v4.4 (10 domains)

结构域编号 domain_id3wtnA00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id3wtnB00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id3wtnC00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id3wtnD00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id3wtnE00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id3wtnF00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id3wtnG00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id3wtnH00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id3wtnI00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id3wtnJ00
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain

8. 引用文献 (1)

9. 文件与曲线 (10)