5qj3

CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH COMPOUND-24 AKA 7-({4-CHLORO-3'-FLUORO-[1,1'- BIPHENYL]-3-YL}METHOXY)-3H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN- 5-AMINE

Method: X-RAY DIFFRACTION Dmax: 111.1 Å Quality: GOOD

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

Myeloperoxidase

Homo sapiens

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 × 2 其他聚合物 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 167–271 链 B; UniProt 278–744 未记录 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;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 CL CHLORIDE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 JXP 7-[(4-chloro-3'-fluoro[1,1'-biphenyl]-3-yl)methoxy]-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;296 K;0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen 分辨率 2.76 Å R-free 0.228
2 其他组合 同源多聚体 蛋白 × 2 其他聚合物 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 D; UniProt 167–271 链 E; UniProt 278–744 未记录 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;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 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;296 K;0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen 分辨率 2.76 Å R-free 0.228

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、107 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 1–105; UniProt 167–271 作者链 D; PDB构建体 1–105; UniProt 167–271 作者链 B; PDB构建体 1–467; UniProt 278–744 作者链 E; PDB构建体 1–467; UniProt 278–744

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 5qj3

P(r) 距离分布 P(r) Distribution

P(r) distribution for 5qj3
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id5qj3
沉积日期 deposition_date2018-09-26
结构标题 titleCRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH COMPOUND-24 AKA 7-({4-CHLORO-3'-FLUORO-[1,1'- BIPHENYL]-3-YL}METHOXY)-3H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN- 5-AMINE
关键词 keywordsMYELOPEROXIDASE, METAL BINDING PROTEIN; METAL 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_guinier33.93
回转半径 Rg (电子) rg_electron33.44
零角强度 I(0) i0272173000.00
分子量 molecular_weight132370.0 kDa
排除体积 excluded_volume165230 ų
包络体积 envelope_volume196080 ų
水化壳体积 shell_volume48326 ų
包络直径 envelope_diameter114.6
壳层 Rg shell_rg40.74
包络 Rg envelope_rg33.53
形状 Rg shape_rg33.42
总 Rg total_rg33.98
总原子数 total_atoms9289
残基数 n_residues1135
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 dmax111.1
Rg (实空间) rg_real33.97
Rg 误差 (实空间) rg_real_error0.87
I(0) (实空间) i0_real2.7220e+08
I(0) 误差 (实空间) i0_real_error4.2330e+06
Rg (倒空间) rg_reciprocal33.95
I(0) (倒空间) i0_reciprocal272200000.0000
解质量估计 total_estimate0.8798
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary35.5
偏度 Skewness skewness0.401
峰度 Kurtosis kurtosis-0.404
角度范围 angular_range— – 0.2350 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha91750000.0000
实空间数据点数 n_real_points48
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.882

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) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id5qj3B00
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_id5qj3E00
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)