5k0b

Crystal Structure of COMT in complex with 2,4-dimethyl-5-[3-(1-phenylethyl)-1H-pyrazol-5-yl]-1,3-thiazole

Method: X-RAY DIFFRACTION Dmax: 154.8 Å Quality: GOOD

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

Catechol O-methyltransferase

Rattus norvegicus

UniProt P22734

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 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 A; UniProt 2–218 未记录 6PS 2,4-dimethyl-5-{3-[(1R)-1-phenylethyl]-1H-pyrazol-5-yl}-1,3-thiazole × 1 PO4 PHOSPHATE ION × 3 K POTASSIUM ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;295 K;0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl 分辨率 2.36 Å R-free 0.195
2 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 B; UniProt 2–218 未记录 6PS 2,4-dimethyl-5-{3-[(1R)-1-phenylethyl]-1H-pyrazol-5-yl}-1,3-thiazole × 1 PO4 PHOSPHATE ION × 4 K POTASSIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;295 K;0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl 分辨率 2.36 Å R-free 0.195
3 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 C; UniProt 2–218 未记录 6PS 2,4-dimethyl-5-{3-[(1R)-1-phenylethyl]-1H-pyrazol-5-yl}-1,3-thiazole × 1 PO4 PHOSPHATE ION × 2 K POTASSIUM ION × 1 CL CHLORIDE ION × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;295 K;0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl 分辨率 2.36 Å R-free 0.195
4 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 D; UniProt 2–218 未记录 6PS 2,4-dimethyl-5-{3-[(1R)-1-phenylethyl]-1H-pyrazol-5-yl}-1,3-thiazole × 1 PO4 PHOSPHATE ION × 1 K POTASSIUM ION × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;295 K;0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl 分辨率 2.36 Å R-free 0.195
5 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 E; UniProt 2–218 未记录 6PS 2,4-dimethyl-5-{3-[(1R)-1-phenylethyl]-1H-pyrazol-5-yl}-1,3-thiazole × 1 PO4 PHOSPHATE ION × 1 K POTASSIUM ION × 1 CL CHLORIDE ION × 2 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;295 K;0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl 分辨率 2.36 Å R-free 0.195
6 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 F; UniProt 2–218 未记录 6PS 2,4-dimethyl-5-{3-[(1R)-1-phenylethyl]-1H-pyrazol-5-yl}-1,3-thiazole × 1 PO4 PHOSPHATE ION × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;295 K;0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl 分辨率 2.36 Å R-free 0.195
7 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 G; UniProt 2–218 未记录 6PS 2,4-dimethyl-5-{3-[(1R)-1-phenylethyl]-1H-pyrazol-5-yl}-1,3-thiazole × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;295 K;0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl 分辨率 2.36 Å R-free 0.195
8 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 H; UniProt 2–218 未记录 6PS 2,4-dimethyl-5-{3-[(1R)-1-phenylethyl]-1H-pyrazol-5-yl}-1,3-thiazole × 1 PO4 PHOSPHATE ION × 2 K POTASSIUM ION × 1 CL CHLORIDE ION × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;295 K;0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl 分辨率 2.36 Å R-free 0.195

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 96 个其他 PDB 条目、153 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 COMT_RAT
Isoform P22734-2
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–217; UniProt 2–218 作者链 B; PDB构建体 1–217; UniProt 2–218 作者链 C; PDB构建体 1–217; UniProt 2–218 作者链 D; PDB构建体 1–217; UniProt 2–218 作者链 E; PDB构建体 1–217; UniProt 2–218 作者链 F; PDB构建体 1–217; UniProt 2–218 作者链 G; PDB构建体 1–217; UniProt 2–218 作者链 H; PDB构建体 1–217; UniProt 2–218

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 5k0b

P(r) 距离分布 P(r) Distribution

P(r) distribution for 5k0b
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id5k0b
沉积日期 deposition_date2016-05-17
结构标题 titleCrystal Structure of COMT in complex with 2,4-dimethyl-5-[3-(1-phenylethyl)-1H-pyrazol-5-yl]-1,3-thiazole
关键词 keywordsMETHYLTRANSFERASE, NEUROTRANSMITTER DEGRADATION, CATECHOL, transferase; TRANSFERASE
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_guinier45.66
回转半径 Rg (电子) rg_electron45.56
零角强度 I(0) i0572311000.00
分子量 molecular_weight198540.0 kDa
排除体积 excluded_volume248560 ų
包络体积 envelope_volume326240 ų
水化壳体积 shell_volume60607 ų
包络直径 envelope_diameter155.1
壳层 Rg shell_rg49.34
包络 Rg envelope_rg44.58
形状 Rg shape_rg45.58
总 Rg total_rg45.67
总原子数 total_atoms13862
残基数 n_residues1722
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 dmax154.8
Rg (实空间) rg_real45.87
Rg 误差 (实空间) rg_real_error1.94
I(0) (实空间) i0_real5.7230e+08
I(0) 误差 (实空间) i0_real_error1.1020e+07
Rg (倒空间) rg_reciprocal45.66
I(0) (倒空间) i0_reciprocal572200000.0000
解质量估计 total_estimate0.8455
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary44.2
偏度 Skewness skewness0.385
峰度 Kurtosis kurtosis-0.613
角度范围 angular_range— – 0.1750 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha42010000.0000
实空间数据点数 n_real_points36
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.750; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.883; Smooth: 0.857

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

6. 实体与聚合物信息 Entities & Polymers (8)

7. 折叠分类 (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

结构域编号 domain_idd5k0ba_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family familyc.66.1.1 — COMT-like
结构域编号 domain_idd5k0bb_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family familyc.66.1.1 — COMT-like
结构域编号 domain_idd5k0bc_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family familyc.66.1.1 — COMT-like
结构域编号 domain_idd5k0bd1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family familyc.66.1.1 — COMT-like
结构域编号 domain_idd5k0bd2
类 Class classl — Artifacts
折叠类型 Fold foldl.1 — Tags
超家族 Superfamily superfamilyl.1.1 — Tags
家族 Family familyl.1.1.1 — Tags
结构域编号 domain_idd5k0be_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family familyc.66.1.1 — COMT-like
结构域编号 domain_idd5k0bf_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family familyc.66.1.1 — COMT-like
结构域编号 domain_idd5k0bg_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family familyc.66.1.1 — COMT-like
结构域编号 domain_idd5k0bh_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
超家族 Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
家族 Family familyc.66.1.1 — COMT-like

CATH v4.4 (8 domains)

结构域编号 domain_id5k0bA01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily150 — Vaccinia Virus protein VP39
结构域编号 domain_id5k0bB01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily150 — Vaccinia Virus protein VP39
结构域编号 domain_id5k0bC01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily150 — Vaccinia Virus protein VP39
结构域编号 domain_id5k0bD01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily150 — Vaccinia Virus protein VP39
结构域编号 domain_id5k0bE01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily150 — Vaccinia Virus protein VP39
结构域编号 domain_id5k0bF01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily150 — Vaccinia Virus protein VP39
结构域编号 domain_id5k0bG01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily150 — Vaccinia Virus protein VP39
结构域编号 domain_id5k0bH01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily150 — Vaccinia Virus protein VP39

8. 引用文献 (1)

9. 文件与曲线 (10)