2c2t

Human Dihydrofolate Reductase Complexed With NADPH and 2,4-Diamino-5-((7,8-dicarbaundecaboran-7-yl)methyl)-6-methylpyrimidine, a novel boron containing, nonclassical Antifolate

Method: X-RAY DIFFRACTION Dmax: 84.1 Å Quality: GOOD

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

DIHYDROFOLATE REDUCTASE

HOMO SAPIENS

UniProt P00374

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 1–186 未记录 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 39B (S)-2,4-DIAMINO-5-((7,8-DICARBAUNDECABORAN-7-YL)METHYL)-6-METHYLPYRIMIDINE × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;THE TERNARY COMPLEX OF DHFR WITH NADPH AND 39B WAS FORMED BY MIXING HUMAN DHFR (20 MG/ML IN 25 MM KPO4 (PH 7.0), 0.1 MM EDTA, AND 3 MM NAN3) WITH 60 MM NADPH, FOLLOWED 15 MINUTES LATER BY 60 MM OF INHIBITOR IN DMSO (FINAL CONCENTRATIONS OF 2 MM NADPH AND 2 MM INHIBITOR). THIS COMPLEX SOLUTION WAS MIXED WITH AN EQUAL VOLUME OF PRECIPITANT CONTAINING 24-33% PEG 4000, 0.2 M LI2SO4, 0.1 M TRIS CL (PH 7.9-8.4), 5% GLYCEROL, AND EQUILIBRATED WITH THE PRECIPITANT BY HANGING DROP VAPOR DIFFUSION AT 277 K. THE CRYSTAL GREW IN ABOUT 3 WEEKS. THE CRYSTAL WAS FLASH-COOLED DIRECTLY IN LIQUID NITROGEN AFTER HARVESTING INTO MOTHER LIQUOR CONTAINING 10% GLYCEROL. NOTE THAT THE INHIBITOR IS ACTUALLY A RACEMIC MIXTURE OF 39B AND ITS ENANTIOMER, HERE CALLED 39E. IT IS THE RACEMATE THAT IS BOUND IN THE CRYSTAL, REPRESENTED IN THE COORDINATES AS A 1:1 STATISTICALLY-DISORDERED MIXTURE OF 39B AND 39E. 分辨率 1.50 Å R-free 0.213
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 1–186 未记录 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 39B (S)-2,4-DIAMINO-5-((7,8-DICARBAUNDECABORAN-7-YL)METHYL)-6-METHYLPYRIMIDINE × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;THE TERNARY COMPLEX OF DHFR WITH NADPH AND 39B WAS FORMED BY MIXING HUMAN DHFR (20 MG/ML IN 25 MM KPO4 (PH 7.0), 0.1 MM EDTA, AND 3 MM NAN3) WITH 60 MM NADPH, FOLLOWED 15 MINUTES LATER BY 60 MM OF INHIBITOR IN DMSO (FINAL CONCENTRATIONS OF 2 MM NADPH AND 2 MM INHIBITOR). THIS COMPLEX SOLUTION WAS MIXED WITH AN EQUAL VOLUME OF PRECIPITANT CONTAINING 24-33% PEG 4000, 0.2 M LI2SO4, 0.1 M TRIS CL (PH 7.9-8.4), 5% GLYCEROL, AND EQUILIBRATED WITH THE PRECIPITANT BY HANGING DROP VAPOR DIFFUSION AT 277 K. THE CRYSTAL GREW IN ABOUT 3 WEEKS. THE CRYSTAL WAS FLASH-COOLED DIRECTLY IN LIQUID NITROGEN AFTER HARVESTING INTO MOTHER LIQUOR CONTAINING 10% GLYCEROL. NOTE THAT THE INHIBITOR IS ACTUALLY A RACEMIC MIXTURE OF 39B AND ITS ENANTIOMER, HERE CALLED 39E. IT IS THE RACEMATE THAT IS BOUND IN THE CRYSTAL, REPRESENTED IN THE COORDINATES AS A 1:1 STATISTICALLY-DISORDERED MIXTURE OF 39B AND 39E. 分辨率 1.50 Å R-free 0.213

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 88 个其他 PDB 条目、104 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 DYR_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–186; UniProt 1–186 作者链 B; PDB构建体 1–186; UniProt 1–186

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 2c2t

P(r) 距离分布 P(r) Distribution

P(r) distribution for 2c2t
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id2c2t
沉积日期 deposition_date2005-09-30
结构标题 titleHuman Dihydrofolate Reductase Complexed With NADPH and 2,4-Diamino-5-((7,8-dicarbaundecaboran-7-yl)methyl)-6-methylpyrimidine, a novel boron containing, nonclassical Antifolate
关键词 keywordsNONCLASSICAL ANTIFOLATES, LIPOPHILIC ANTIFOLATES, NADP, ONE- CARBON METABOLISM, OXIDOREDUCTASE, REDUCTASE; 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_guinier25.70
回转半径 Rg (电子) rg_electron24.95
零角强度 I(0) i032657300.00
分子量 molecular_weight44743.0 kDa
排除体积 excluded_volume56288 ų
包络体积 envelope_volume69270 ų
水化壳体积 shell_volume23930 ų
包络直径 envelope_diameter86.3
壳层 Rg shell_rg31.28
包络 Rg envelope_rg25.03
形状 Rg shape_rg24.93
总 Rg total_rg25.76
总原子数 total_atoms3148
残基数 n_residues372
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 dmax84.1
Rg (实空间) rg_real25.79
Rg 误差 (实空间) rg_real_error0.56
I(0) (实空间) i0_real3.2660e+07
I(0) 误差 (实空间) i0_real_error4.5800e+05
Rg (倒空间) rg_reciprocal25.77
I(0) (倒空间) i0_reciprocal32660000.0000
解质量估计 total_estimate0.8777
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary25.8
偏度 Skewness skewness0.421
峰度 Kurtosis kurtosis-0.466
角度范围 angular_range— – 0.3100 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha7598000.0000
实空间数据点数 n_real_points63
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.971

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

6. 实体与聚合物信息 Entities & Polymers (5)

7. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_idd2c2ta_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.71 — Dihydrofolate reductase-like
超家族 Superfamily superfamilyc.71.1 — Dihydrofolate reductase-like
家族 Family familyc.71.1.1 — Dihydrofolate reductases
结构域编号 domain_idd2c2tb_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.71 — Dihydrofolate reductase-like
超家族 Superfamily superfamilyc.71.1 — Dihydrofolate reductase-like
家族 Family familyc.71.1.1 — Dihydrofolate reductases

CATH v4.4 (2 domains)

结构域编号 domain_id2c2tA00
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology430 — Dihydrofolate Reductase, subunit A
同源超家族 H-superfamily homologous superfamily10 — Dihydrofolate Reductase, subunit A
结构域编号 domain_id2c2tB00
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology430 — Dihydrofolate Reductase, subunit A
同源超家族 H-superfamily homologous superfamily10 — Dihydrofolate Reductase, subunit A

8. 引用文献 (1)

9. 文件与曲线 (10)