6av7

Structure of human endothelial nitric oxide synthase heme domain in complex with HW69

Method: X-RAY DIFFRACTION Dmax: 144.3 Å Quality: GOOD

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

Nitric oxide synthase, endothelial

Homo sapiens

UniProt P29474

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 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 41–480 链 B; UniProt 41–480 片段:UNP residues 41-480 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 H4B 5,6,7,8-TETRAHYDROBIOPTERIN × 2 W69 6-(2-{3-[3-(dimethylamino)propyl]-5-fluorophenyl}ethyl)-4-methylpyridin-2-amine × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 ZN ZINC ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 GD GADOLINIUM ATOM × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;12-15% PEG3350, 0.1M BIS-TRIS 0.2-0.3M MG ACETATE, 0.1M GdCl3 10% glycerol, 5 MM TCEP 分辨率 1.92 Å R-free 0.254
2 蛋白同源多聚体 同源多聚体 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 C; UniProt 41–480 链 D; UniProt 41–480 片段:UNP residues 41-480 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 H4B 5,6,7,8-TETRAHYDROBIOPTERIN × 2 W69 6-(2-{3-[3-(dimethylamino)propyl]-5-fluorophenyl}ethyl)-4-methylpyridin-2-amine × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 5 ZN ZINC ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 GD GADOLINIUM ATOM × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;12-15% PEG3350, 0.1M BIS-TRIS 0.2-0.3M MG ACETATE, 0.1M GdCl3 10% glycerol, 5 MM TCEP 分辨率 1.92 Å R-free 0.254

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 94 个其他 PDB 条目、182 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 NOS3_HUMAN
Isoform P29474-3
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–440; UniProt 41–480 作者链 B; PDB构建体 1–440; UniProt 41–480 作者链 C; PDB构建体 1–440; UniProt 41–480 作者链 D; PDB构建体 1–440; UniProt 41–480

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 6av7

P(r) 距离分布 P(r) Distribution

P(r) distribution for 6av7
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id6av7
沉积日期 deposition_date2017-09-01
结构标题 titleStructure of human endothelial nitric oxide synthase heme domain in complex with HW69
关键词 keywordsnitric oxide synthase inhibitor complex heme enzyme, OXIDOREDUCTASE; OXIDOREDUCTASE
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_guinier43.44
回转半径 Rg (电子) rg_electron43.01
零角强度 I(0) i0533382000.00
分子量 molecular_weight189660.0 kDa
排除体积 excluded_volume236470 ų
包络体积 envelope_volume304110 ų
水化壳体积 shell_volume58925 ų
包络直径 envelope_diameter150.8
壳层 Rg shell_rg47.71
包络 Rg envelope_rg42.81
形状 Rg shape_rg43.05
总 Rg total_rg43.06
总原子数 total_atoms13326
残基数 n_residues1609
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 dmax144.3
Rg (实空间) rg_real43.49
Rg 误差 (实空间) rg_real_error1.60
I(0) (实空间) i0_real5.3340e+08
I(0) 误差 (实空间) i0_real_error9.5140e+06
Rg (倒空间) rg_reciprocal43.44
I(0) (倒空间) i0_reciprocal533300000.0000
解质量估计 total_estimate0.8820
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary40.1
偏度 Skewness skewness0.290
峰度 Kurtosis kurtosis-0.598
角度范围 angular_range— – 0.1800 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha137800000.0000
实空间数据点数 n_real_points37
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.836

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

6. 实体与聚合物信息 Entities & Polymers (10)

7. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

结构域编号 domain_idd6av7a_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.174 — Nitric oxide (NO) synthase oxygenase domain
超家族 Superfamily superfamilyd.174.1 — Nitric oxide (NO) synthase oxygenase domain
家族 Family familyd.174.1.1 — Nitric oxide (NO) synthase oxygenase domain
结构域编号 domain_idd6av7b_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.174 — Nitric oxide (NO) synthase oxygenase domain
超家族 Superfamily superfamilyd.174.1 — Nitric oxide (NO) synthase oxygenase domain
家族 Family familyd.174.1.1 — Nitric oxide (NO) synthase oxygenase domain
结构域编号 domain_idd6av7c_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.174 — Nitric oxide (NO) synthase oxygenase domain
超家族 Superfamily superfamilyd.174.1 — Nitric oxide (NO) synthase oxygenase domain
家族 Family familyd.174.1.1 — Nitric oxide (NO) synthase oxygenase domain
结构域编号 domain_idd6av7d_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.174 — Nitric oxide (NO) synthase oxygenase domain
超家族 Superfamily superfamilyd.174.1 — Nitric oxide (NO) synthase oxygenase domain
家族 Family familyd.174.1.1 — Nitric oxide (NO) synthase oxygenase domain

CATH v4.4 (12 domains)

结构域编号 domain_id6av7A01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology340 — Nitric Oxide Synthase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 1
结构域编号 domain_id6av7A02
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology440 — Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase;Heme Domain;Chain A domain 2
结构域编号 domain_id6av7A03
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1230 — Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 3
结构域编号 domain_id6av7B01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology340 — Nitric Oxide Synthase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 1
结构域编号 domain_id6av7B02
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology440 — Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase;Heme Domain;Chain A domain 2
结构域编号 domain_id6av7B03
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1230 — Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 3
结构域编号 domain_id6av7C01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology340 — Nitric Oxide Synthase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 1
结构域编号 domain_id6av7C02
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology440 — Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase;Heme Domain;Chain A domain 2
结构域编号 domain_id6av7C03
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1230 — Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 3
结构域编号 domain_id6av7D01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology340 — Nitric Oxide Synthase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 1
结构域编号 domain_id6av7D02
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology440 — Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase;Heme Domain;Chain A domain 2
结构域编号 domain_id6av7D03
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1230 — Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
同源超家族 H-superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 3

8. 引用文献 (1)

9. 文件与曲线 (10)