5lxb

Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with palonosetron

Method: X-RAY DIFFRACTION Dmax: 144.7 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 1–236 链 B; UniProt 1–236 链 C; UniProt 1–236 链 D; UniProt 1–236 链 E; UniProt 1–236 未记录 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 7A9 palonosetron × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;293 K;200 mM sodium 265 citrate, 100 mM bis tris propane pH 8.5, and 20% (w/v) PEG3350. 分辨率 2.34 Å R-free 0.245
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 1–236 链 G; UniProt 1–236 链 H; UniProt 1–236 链 I; UniProt 1–236 链 J; UniProt 1–236 未记录 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 7A9 palonosetron × 3 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;293 K;200 mM sodium 265 citrate, 100 mM bis tris propane pH 8.5, and 20% (w/v) PEG3350. 分辨率 2.34 Å R-free 0.245

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 1–236; UniProt 1–236 作者链 B; PDB构建体 1–236; UniProt 1–236 作者链 C; PDB构建体 1–236; UniProt 1–236 作者链 D; PDB构建体 1–236; UniProt 1–236 作者链 E; PDB构建体 1–236; UniProt 1–236 作者链 F; PDB构建体 1–236; UniProt 1–236 作者链 G; PDB构建体 1–236; UniProt 1–236 作者链 H; PDB构建体 1–236; UniProt 1–236 作者链 I; PDB构建体 1–236; UniProt 1–236 作者链 J; PDB构建体 1–236; UniProt 1–236

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 5lxb

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id5lxb
沉积日期 deposition_date2016-09-20
结构标题 titleCrystal structure of a mutant binding protein (5HTBP-AChBP) in complex with palonosetron
关键词 keywordsCys-loop receptor, 5-HT3 receptor, 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_guinier46.86
回转半径 Rg (电子) rg_electron46.61
零角强度 I(0) i0818110000.00
分子量 molecular_weight236680.0 kDa
排除体积 excluded_volume295620 ų
包络体积 envelope_volume407940 ų
水化壳体积 shell_volume73788 ų
包络直径 envelope_diameter158.3
壳层 Rg shell_rg49.96
包络 Rg envelope_rg45.73
形状 Rg shape_rg46.61
总 Rg total_rg46.77
总原子数 total_atoms16666
残基数 n_residues2050
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 dmax144.7
Rg (实空间) rg_real47.06
Rg 误差 (实空间) rg_real_error1.16
I(0) (实空间) i0_real8.1810e+08
I(0) 误差 (实空间) i0_real_error1.5370e+07
Rg (倒空间) rg_reciprocal46.86
I(0) (倒空间) i0_reciprocal817900000.0000
解质量估计 total_estimate0.8183
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary46.8
偏度 Skewness skewness0.448
峰度 Kurtosis kurtosis-0.472
角度范围 angular_range— – 0.1700 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha163100000.0000
实空间数据点数 n_real_points35
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.068

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

6. 实体与聚合物信息 Entities & Polymers (4)

7. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_idd5lxba_
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_idd5lxbb_
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_idd5lxbc_
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_idd5lxbd_
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_idd5lxbe_
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_idd5lxbf_
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_idd5lxbg_
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_idd5lxbh_
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_idd5lxbi_
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_idd5lxbj_
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

CATH v4.4 (10 domains)

结构域编号 domain_id5lxbA00
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_id5lxbB00
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_id5lxbC00
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_id5lxbD00
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_id5lxbE00
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_id5lxbF00
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_id5lxbG00
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_id5lxbH00
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_id5lxbI00
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_id5lxbJ00
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)