3b2v

Crystal structure of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of IMC-11F8

Method: X-RAY DIFFRACTION Dmax: 151.5 Å Quality: REASONABLE

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

Epidermal growth factor receptor

Homo sapiens

UniProt P00533

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 异源复合物 蛋白 × 3 其他聚合物 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 A; UniProt 25–642 片段:Extracellular domain IMC-11F8 FAB Light chain × 1 IMC-11F8 FAB Heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.5;298 K;12 % PEG 3350, IM NaCl, 50 mM MES, pH 6.5, vapor diffusion, temperature 298K 分辨率 3.30 Å R-free 0.367

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 383 个其他 PDB 条目、565 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 EGFR_HUMAN
Isoform
PDB实体 3
链与序列区间 作者链 A; PDB构建体 1–618; UniProt 25–642

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 3b2v

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3b2v
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3b2v
沉积日期 deposition_date2007-10-19
结构标题 titleCrystal structure of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of IMC-11F8
关键词 keywords;CELL SURFACE RECEPTOR; GLYCOPROTEIN; ANTIGEN:ANTIBODY COMPLEX; FAB FRAGMENT; ANTITUMOR; DRUG, Anti-oncogene, ATP-binding, Cell cycle, Disease mutation, Kinase, Membrane, Nucleotide-binding, Phosphoprotein, Secreted, Transferase, Transmembrane, Tyrosine-protein kinase, IMMUNE SYSTEM-TRANSFERASE COMPLEX ;; IMMUNE SYSTEM/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_guinier39.82
回转半径 Rg (电子) rg_electron40.17
零角强度 I(0) i0115082000.00
分子量 molecular_weight80582.0 kDa
排除体积 excluded_volume98346 ų
包络体积 envelope_volume147970 ų
水化壳体积 shell_volume35122 ų
包络直径 envelope_diameter157.7
壳层 Rg shell_rg38.51
包络 Rg envelope_rg42.07
形状 Rg shape_rg40.10
总 Rg total_rg40.28
总原子数 total_atoms5645
残基数 n_residues805
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 dmax151.5
Rg (实空间) rg_real40.90
Rg 误差 (实空间) rg_real_error1.87
I(0) (实空间) i0_real1.1510e+08
I(0) 误差 (实空间) i0_real_error2.5820e+06
Rg (倒空间) rg_reciprocal40.23
I(0) (倒空间) i0_reciprocal115000000.0000
解质量估计 total_estimate0.7109
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary34.1
偏度 Skewness skewness0.787
峰度 Kurtosis kurtosis0.131
角度范围 angular_range— – 0.2000 −1
当前正则化参数 α current_alpha0.0001
最高正则化参数 α highest_alpha9597000.0000
实空间数据点数 n_real_points41
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.427; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.271; Smooth: 0.684

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

6. 实体与聚合物信息 Entities & Polymers (6)

7. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (3 domains)

结构域编号 domain_idd3b2vh1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.1 — V set domains (antibody variable domain-like)
结构域编号 domain_idd3b2vh2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
结构域编号 domain_idd3b2vh3
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

CATH v4.4 (8 domains)

结构域编号 domain_id3b2vA01
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
同源超家族 H-superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
结构域编号 domain_id3b2vA02
类 Class class3 — Alpha Beta
架构 Architecture architecture80 — Alpha-Beta Horseshoe
拓扑 Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
同源超家族 H-superfamily homologous superfamily20 — Receptor L-domain
结构域编号 domain_id3b2vA03
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
同源超家族 H-superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
结构域编号 domain_id3b2vA04
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
同源超家族 H-superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
结构域编号 domain_id3b2vH01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3b2vH02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3b2vL01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3b2vL02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins

8. 引用文献 (1)

9. 文件与曲线 (10)