1dnw

HUMAN MYELOPEROXIDASE-CYANIDE-THIOCYANATE COMPLEX

Method: X-RAY DIFFRACTION Dmax: 110.7 Å Quality: GOOD

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

MYELOPEROXIDASE

物种未注明

UniProt P05164

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 其他组合 同源多聚体 蛋白 × 4 其他聚合物 2 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 A; UniProt 167–270 链 B; UniProt 167–270 链 C; UniProt 279–744 链 D; UniProt 279–744 片段:MYELOPEROXIDASE LIGHT CHAIN CONTAINING RESIDUES 1 TO 104 片段:MYELOPEROXIDASE HEAVY CHAIN CONTAINING RESIDUES 113 TO 578 非标准单体:是(mmCIF未提供具体位点) ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 SCN THIOCYANATE ION × 4 SO4 SULFATE ION × 3 CYN CYANIDE ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ACY ACETIC ACID × 6 X-RAY DIFFRACTION X-ray结晶条件:Vapor Diffusion, Hanging Drop with Macro Seeding;pH 5.5;295 K;Co-crystal grown from sodium cyanide, sodium acetate, ammonium, sulfate, calcium chloride, and PEG MW 8000. It was subsequently equilibrated with a substitute mother liquor containing sodium thiocyanate, pH 5.5, Vapor Diffusion, Hanging Drop with Macro Seeding, temperature 22K 分辨率 1.90 Å R-free 0.224
2 其他组合 同源多聚体 蛋白 × 2 其他聚合物 1 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 167–270 链 C; UniProt 279–744 片段:MYELOPEROXIDASE LIGHT CHAIN CONTAINING RESIDUES 1 TO 104 片段:MYELOPEROXIDASE HEAVY CHAIN CONTAINING RESIDUES 113 TO 578 非标准单体:是(mmCIF未提供具体位点) ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 SCN THIOCYANATE ION × 2 SO4 SULFATE ION × 2 CYN CYANIDE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACY ACETIC ACID × 3 X-RAY DIFFRACTION X-ray结晶条件:Vapor Diffusion, Hanging Drop with Macro Seeding;pH 5.5;295 K;Co-crystal grown from sodium cyanide, sodium acetate, ammonium, sulfate, calcium chloride, and PEG MW 8000. It was subsequently equilibrated with a substitute mother liquor containing sodium thiocyanate, pH 5.5, Vapor Diffusion, Hanging Drop with Macro Seeding, temperature 22K 分辨率 1.90 Å R-free 0.224
3 其他组合 同源多聚体 蛋白 × 2 其他聚合物 1 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 B; UniProt 167–270 链 D; UniProt 279–744 片段:MYELOPEROXIDASE LIGHT CHAIN CONTAINING RESIDUES 1 TO 104 片段:MYELOPEROXIDASE HEAVY CHAIN CONTAINING RESIDUES 113 TO 578 非标准单体:是(mmCIF未提供具体位点) ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 SCN THIOCYANATE ION × 2 SO4 SULFATE ION × 1 CYN CYANIDE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACY ACETIC ACID × 3 X-RAY DIFFRACTION X-ray结晶条件:Vapor Diffusion, Hanging Drop with Macro Seeding;pH 5.5;295 K;Co-crystal grown from sodium cyanide, sodium acetate, ammonium, sulfate, calcium chloride, and PEG MW 8000. It was subsequently equilibrated with a substitute mother liquor containing sodium thiocyanate, pH 5.5, Vapor Diffusion, Hanging Drop with Macro Seeding, temperature 22K 分辨率 1.90 Å R-free 0.224

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 48 个其他 PDB 条目、106 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 PERM_HUMAN
Isoform
PDB实体 1, 2
链与序列区间 作者链 A; PDB构建体 1–104; UniProt 167–270 作者链 B; PDB构建体 1–104; UniProt 167–270 作者链 C; PDB构建体 1–466; UniProt 279–744 作者链 D; PDB构建体 1–466; UniProt 279–744

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 1dnw

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1dnw
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1dnw
沉积日期 deposition_date1999-12-16
结构标题 titleHUMAN MYELOPEROXIDASE-CYANIDE-THIOCYANATE COMPLEX
关键词 keywordsoxidoreductase, peroxidase, substrate complex, thiocyanate, halide peroxidation; 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_guinier34.05
回转半径 Rg (电子) rg_electron33.43
零角强度 I(0) i0293125000.00
分子量 molecular_weight135360.0 kDa
排除体积 excluded_volume168230 ų
包络体积 envelope_volume201010 ų
水化壳体积 shell_volume49274 ų
包络直径 envelope_diameter119.2
壳层 Rg shell_rg40.90
包络 Rg envelope_rg33.56
形状 Rg shape_rg33.41
总 Rg total_rg34.01
总原子数 total_atoms9487
残基数 n_residues1138
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 dmax110.7
Rg (实空间) rg_real34.08
Rg 误差 (实空间) rg_real_error0.70
I(0) (实空间) i0_real2.9310e+08
I(0) 误差 (实空间) i0_real_error4.9440e+06
Rg (倒空间) rg_reciprocal34.06
I(0) (倒空间) i0_reciprocal293100000.0000
解质量估计 total_estimate0.8835
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary36.1
偏度 Skewness skewness0.390
峰度 Kurtosis kurtosis-0.417
角度范围 angular_range— – 0.2300 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha109000000.0000
实空间数据点数 n_real_points47
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.871

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

6. 实体与聚合物信息 Entities & Polymers (11)

7. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_idd1dnw.1
类 Class classa — All alpha proteins
折叠类型 Fold folda.93 — Heme-dependent peroxidases
超家族 Superfamily superfamilya.93.1 — Heme-dependent peroxidases
家族 Family familya.93.1.2 — Myeloperoxidase-like
结构域编号 domain_idd1dnw.2
类 Class classa — All alpha proteins
折叠类型 Fold folda.93 — Heme-dependent peroxidases
超家族 Superfamily superfamilya.93.1 — Heme-dependent peroxidases
家族 Family familya.93.1.2 — Myeloperoxidase-like

CATH v4.4 (2 domains)

结构域编号 domain_id1dnwC00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology640 — Myeloperoxidase, subunit C
同源超家族 H-superfamily homologous superfamily10 — Haem peroxidase domain superfamily, animal type
结构域编号 domain_id1dnwD00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology640 — Myeloperoxidase, subunit C
同源超家族 H-superfamily homologous superfamily10 — Haem peroxidase domain superfamily, animal type

8. 引用文献 (1)

9. 文件与曲线 (10)