5brx

X-ray crystal structure of Aplysia californica (Ac-AChBP) in complex with 2-pyridyl azatricyclo[3.3.1.13,7]decane; 2-pyridylazaadamantane; 2-Aza (TI-8480)

Method: X-RAY DIFFRACTION Dmax: 137.8 Å Quality: GOOD

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

Soluble acetylcholine receptor

Aplysia californica

UniProt Q8WSF8

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 18–236 链 B; UniProt 18–236 链 C; UniProt 18–236 链 D; UniProt 18–236 链 E; UniProt 18–236 片段:UNP residues 18-236 突变:Y55W SO4 SULFATE ION × 5 TI4 (2R,3S,5R,7S)-2-(pyridin-3-yl)-1-azatricyclo[3.3.1.1~3,7~]decane × 2 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;1.7% PEG 400, 0.085 M HEPES - Na pH 7.5, 1.7 M Ammonium Sulfate, 15% Glycerol 分辨率 2.05 Å R-free 0.235
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 18–236 链 G; UniProt 18–236 链 H; UniProt 18–236 链 I; UniProt 18–236 链 J; UniProt 18–236 片段:UNP residues 18-236 突变:Y55W SO4 SULFATE ION × 5 TI4 (2R,3S,5R,7S)-2-(pyridin-3-yl)-1-azatricyclo[3.3.1.1~3,7~]decane × 2 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;1.7% PEG 400, 0.085 M HEPES - Na pH 7.5, 1.7 M Ammonium Sulfate, 15% Glycerol 分辨率 2.05 Å R-free 0.235

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 85 个其他 PDB 条目、119 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 Q8WSF8_APLCA
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 10–228; UniProt 18–236 作者链 B; PDB构建体 10–228; UniProt 18–236 作者链 C; PDB构建体 10–228; UniProt 18–236 作者链 D; PDB构建体 10–228; UniProt 18–236 作者链 E; PDB构建体 10–228; UniProt 18–236 作者链 F; PDB构建体 10–228; UniProt 18–236 作者链 G; PDB构建体 10–228; UniProt 18–236 作者链 H; PDB构建体 10–228; UniProt 18–236 作者链 I; PDB构建体 10–228; UniProt 18–236 作者链 J; PDB构建体 10–228; UniProt 18–236

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 5brx

P(r) 距离分布 P(r) Distribution

P(r) distribution for 5brx
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id5brx
沉积日期 deposition_date2015-06-01
结构标题 titleX-ray crystal structure of Aplysia californica (Ac-AChBP) in complex with 2-pyridyl azatricyclo[3.3.1.13,7]decane; 2-pyridylazaadamantane; 2-Aza (TI-8480)
关键词 keywordsAChBP, nicotine, acetylcholine, ACETYLCHOLINE BINDING PROTEIN; ACETYLCHOLINE BINDING 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_guinier42.72
回转半径 Rg (电子) rg_electron41.91
零角强度 I(0) i0849172000.00
分子量 molecular_weight234760.0 kDa
排除体积 excluded_volume291320 ų
包络体积 envelope_volume405850 ų
水化壳体积 shell_volume80822 ų
包络直径 envelope_diameter141.0
壳层 Rg shell_rg47.82
包络 Rg envelope_rg39.81
形状 Rg shape_rg41.87
总 Rg total_rg42.36
总原子数 total_atoms16712
残基数 n_residues2105
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 dmax137.8
Rg (实空间) rg_real42.58
Rg 误差 (实空间) rg_real_error1.02
I(0) (实空间) i0_real8.4920e+08
I(0) 误差 (实空间) i0_real_error1.3550e+07
Rg (倒空间) rg_reciprocal42.72
I(0) (倒空间) i0_reciprocal849300000.0000
解质量估计 total_estimate0.8775
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary52.1
偏度 Skewness skewness0.245
峰度 Kurtosis kurtosis-0.391
角度范围 angular_range— – 0.1850 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha119600000.0000
实空间数据点数 n_real_points38
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.904

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_idd5brxa1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxa2
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_idd5brxb1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxb2
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_idd5brxc1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxc2
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_idd5brxd1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxd2
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_idd5brxe1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxe2
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_idd5brxf1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxf2
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_idd5brxg1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxg2
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_idd5brxh1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxh2
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_idd5brxi1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxi2
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_idd5brxj1
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.96.1.0 — automated matches
结构域编号 domain_idd5brxj2
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_id5brxA00
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_id5brxB00
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_id5brxC00
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_id5brxD00
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_id5brxE00
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_id5brxF00
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_id5brxG00
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_id5brxH00
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_id5brxI00
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_id5brxJ00
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)