4um1

Engineered Ls-AChBP with alpha4-alpha4 binding pocket in complex with NS3573

Method: X-RAY DIFFRACTION Dmax: 89.1 Å Quality: EXCELLENT

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 1–229 链 B; UniProt 1–229 链 C; UniProt 1–229 链 D; UniProt 1–229 链 E; UniProt 1–229 突变:YES 09P 1-(5-ethoxypyridin-3-yl)-1,4-diazepane × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray结晶条件:pH 8;0.1 M TRIS BASE (PH 8.0), 1-3% V/V POLYETHYLENE GLYCOL (PEG) 400 AND 1.8-2.3 M (NH4)2SO4 分辨率 2.83 Å R-free 0.231

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、122 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 1–229; UniProt 1–229 作者链 B; PDB构建体 1–229; UniProt 1–229 作者链 C; PDB构建体 1–229; UniProt 1–229 作者链 D; PDB构建体 1–229; UniProt 1–229 作者链 E; PDB构建体 1–229; UniProt 1–229

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 4um1

P(r) 距离分布 P(r) Distribution

P(r) distribution for 4um1
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id4um1
沉积日期 deposition_date2014-05-14
结构标题 titleEngineered Ls-AChBP with alpha4-alpha4 binding pocket in complex with NS3573
关键词 keywordsSIGNALING PROTEIN, ION CHANNEL, RECEPTOR STOICHIOMETRY, CYS-LOOP RECEPTOR, ACETYLCHOLINE BINDING 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_guinier31.26
回转半径 Rg (电子) rg_electron29.96
零角强度 I(0) i0414321000.00
分子量 molecular_weight107060.0 kDa
排除体积 excluded_volume102810 ų
包络体积 envelope_volume188100 ų
水化壳体积 shell_volume49741 ų
包络直径 envelope_diameter96.7
壳层 Rg shell_rg39.23
包络 Rg envelope_rg29.16
形状 Rg shape_rg29.90
总 Rg total_rg30.69
总原子数 total_atoms8114
残基数 n_residues1004
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 dmax89.1
Rg (实空间) rg_real30.94
Rg 误差 (实空间) rg_real_error0.36
I(0) (实空间) i0_real4.1430e+08
I(0) 误差 (实空间) i0_real_error5.0240e+06
Rg (倒空间) rg_reciprocal31.08
I(0) (倒空间) i0_reciprocal414400000.0000
解质量估计 total_estimate0.9031
解质量评级 solution_quality EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary43.7
偏度 Skewness skewness-0.083
峰度 Kurtosis kurtosis-0.595
角度范围 angular_range— – 0.2550 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha80770000.0000
实空间数据点数 n_real_points52
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.950

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) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_idd4um1a_
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_idd4um1b_
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_idd4um1c_
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_idd4um1d_
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_idd4um1e_
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

CATH v4.4 (5 domains)

结构域编号 domain_id4um1A00
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_id4um1B00
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_id4um1C00
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_id4um1D00
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_id4um1E00
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)