5j5g

X-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) in Complex with 6-(4-methoxyphenyl)-N4,N4-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine

Method: X-RAY DIFFRACTION Dmax: 133.3 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 20–229 链 B; UniProt 20–229 链 C; UniProt 20–229 链 D; UniProt 20–229 链 E; UniProt 20–229 未记录 PO4 PHOSPHATE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 6GF 6-(4-methoxyphenyl)-N~4~,N~4~-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine × 5 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 5;290 K;0.26 M ammonium phosphate monobasic, 35% v/v glycerol 分辨率 2.04 Å R-free 0.209
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 20–229 链 G; UniProt 20–229 链 H; UniProt 20–229 链 I; UniProt 20–229 链 J; UniProt 20–229 未记录 PO4 PHOSPHATE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 6GF 6-(4-methoxyphenyl)-N~4~,N~4~-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine × 5 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 5;290 K;0.26 M ammonium phosphate monobasic, 35% v/v glycerol 分辨率 2.04 Å R-free 0.209

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、121 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 9–218; UniProt 20–229 作者链 B; PDB构建体 9–218; UniProt 20–229 作者链 C; PDB构建体 9–218; UniProt 20–229 作者链 D; PDB构建体 9–218; UniProt 20–229 作者链 E; PDB构建体 9–218; UniProt 20–229 作者链 F; PDB构建体 9–218; UniProt 20–229 作者链 G; PDB构建体 9–218; UniProt 20–229 作者链 H; PDB构建体 9–218; UniProt 20–229 作者链 I; PDB构建体 9–218; UniProt 20–229 作者链 J; PDB构建体 9–218; 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。

SAXS 散射曲线 SAXS Profile

SAXS profile for 5j5g

P(r) 距离分布 P(r) Distribution

P(r) distribution for 5j5g
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id5j5g
沉积日期 deposition_date2016-04-02
结构标题 titleX-Ray Crystal Structure of Acetylcholine Binding Protein (AChBP) in Complex with 6-(4-methoxyphenyl)-N4,N4-bis[(pyridin-2-yl)methyl]pyrimidine-2,4-diamine
关键词 keywordsAcetylcholine-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_guinier41.70
回转半径 Rg (电子) rg_electron40.95
零角强度 I(0) i01002320000.00
分子量 molecular_weight251370.0 kDa
排除体积 excluded_volume310550 ų
包络体积 envelope_volume410190 ų
水化壳体积 shell_volume81093 ų
包络直径 envelope_diameter150.3
壳层 Rg shell_rg48.23
包络 Rg envelope_rg39.97
形状 Rg shape_rg40.92
总 Rg total_rg41.39
总原子数 total_atoms17714
残基数 n_residues2149
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 dmax133.3
Rg (实空间) rg_real41.54
Rg 误差 (实空间) rg_real_error0.99
I(0) (实空间) i0_real1.0020e+09
I(0) 误差 (实空间) i0_real_error1.7720e+07
Rg (倒空间) rg_reciprocal41.70
I(0) (倒空间) i0_reciprocal1002000000.0000
解质量估计 total_estimate0.8040
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary52.6
偏度 Skewness skewness0.236
峰度 Kurtosis kurtosis-0.289
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_alpha109100000.0000
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: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.000

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_idd5j5ga1
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_idd5j5ga2
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_idd5j5gb1
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_idd5j5gb2
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_idd5j5gc1
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_idd5j5gc2
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_idd5j5gd1
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_idd5j5gd2
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_idd5j5ge1
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_idd5j5ge2
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_idd5j5gf1
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_idd5j5gf2
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_idd5j5gg1
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_idd5j5gg2
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_idd5j5gh1
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_idd5j5gh2
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_idd5j5gi1
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_idd5j5gi2
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_idd5j5gj1
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_idd5j5gj2
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_id5j5gA00
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_id5j5gB00
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_id5j5gC00
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_id5j5gD00
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_id5j5gE00
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_id5j5gF00
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_id5j5gG00
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_id5j5gH00
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_id5j5gI00
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_id5j5gJ00
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)