6yxv

FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-Methyl-N-{3-[(2-phenylamino-5-trifluoromethyl-pyrimidin-4-ylamino)-methyl]-pyridin-2-yl}-methanesulfonamide

Method: X-RAY DIFFRACTION Dmax: 127.5 Å Quality: GOOD

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

Focal adhesion kinase 1

Homo sapiens

UniProt Q05397

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 411–689 未记录 Q2H ~{N}-methyl-~{N}-[3-[(~{E})-[2-phenylazanyl-5-(trifluoromethyl)pyrimidin-4-yl]iminomethyl]pyridin-2-yl]methanesulfonamide × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;294 K;15% PEG 3350 分辨率 2.30 Å R-free 0.232
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 411–689 未记录 Q2H ~{N}-methyl-~{N}-[3-[(~{E})-[2-phenylazanyl-5-(trifluoromethyl)pyrimidin-4-yl]iminomethyl]pyridin-2-yl]methanesulfonamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;294 K;15% PEG 3350 分辨率 2.30 Å R-free 0.232
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 411–689 未记录 Q2H ~{N}-methyl-~{N}-[3-[(~{E})-[2-phenylazanyl-5-(trifluoromethyl)pyrimidin-4-yl]iminomethyl]pyridin-2-yl]methanesulfonamide × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;294 K;15% PEG 3350 分辨率 2.30 Å R-free 0.232
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 411–689 未记录 Q2H ~{N}-methyl-~{N}-[3-[(~{E})-[2-phenylazanyl-5-(trifluoromethyl)pyrimidin-4-yl]iminomethyl]pyridin-2-yl]methanesulfonamide × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;294 K;15% PEG 3350 分辨率 2.30 Å R-free 0.232

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 38 个其他 PDB 条目、78 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 FAK1_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 4–282; UniProt 411–689 作者链 B; PDB构建体 4–282; UniProt 411–689 作者链 C; PDB构建体 4–282; UniProt 411–689 作者链 D; PDB构建体 4–282; UniProt 411–689

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 6yxv

P(r) 距离分布 P(r) Distribution

P(r) distribution for 6yxv
下载 Download

2. 结构基本信息 2. Structure Basics

条目编号 entry_id6yxv
沉积日期 deposition_date2020-05-04
结构标题 titleFOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-Methyl-N-{3-[(2-phenylamino-5-trifluoromethyl-pyrimidin-4-ylamino)-methyl]-pyridin-2-yl}-methanesulfonamide
关键词 keywordsPROTEIN TYROSINE KINASE, ATP BINDING, TRANSFERASE, TRANSFERASE-INHIBITOR COMPLEX; 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_guinier37.62
回转半径 Rg (电子) rg_electron37.40
零角强度 I(0) i0223068000.00
分子量 molecular_weight121480.0 kDa
排除体积 excluded_volume152460 ų
包络体积 envelope_volume201250 ų
水化壳体积 shell_volume46368 ų
包络直径 envelope_diameter128.2
壳层 Rg shell_rg41.34
包络 Rg envelope_rg37.26
形状 Rg shape_rg37.41
总 Rg total_rg37.59
总原子数 total_atoms8516
残基数 n_residues1043
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 dmax127.5
Rg (实空间) rg_real37.73
Rg 误差 (实空间) rg_real_error1.15
I(0) (实空间) i0_real2.2310e+08
I(0) 误差 (实空间) i0_real_error3.8650e+06
Rg (倒空间) rg_reciprocal37.67
I(0) (倒空间) i0_reciprocal223100000.0000
解质量估计 total_estimate0.8702
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary42.5
偏度 Skewness skewness0.396
峰度 Kurtosis kurtosis-0.307
角度范围 angular_range— – 0.2100 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha25600000.0000
实空间数据点数 n_real_points43
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.711

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

6. 实体与聚合物信息 Entities & Polymers (4)

7. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_idd6yxva_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
家族 Family familyd.144.1.7 — Protein kinases, catalytic subunit
结构域编号 domain_idd6yxvb_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
家族 Family familyd.144.1.7 — Protein kinases, catalytic subunit
结构域编号 domain_idd6yxvc_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
家族 Family familyd.144.1.7 — Protein kinases, catalytic subunit
结构域编号 domain_idd6yxvd_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
家族 Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (8 domains)

结构域编号 domain_id6yxvA01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id6yxvA02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id6yxvB01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id6yxvB02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id6yxvC01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id6yxvC02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id6yxvD01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id6yxvD02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. 引用文献 (1)

9. 文件与曲线 (10)