1bbz

CRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN COMPLEXED WITH A DESIGNED HIGH-AFFINITY PEPTIDE LIGAND: IMPLICATIONS FOR SH3-LIGAND INTERACTIONS

Method: X-RAY DIFFRACTION Dmax: 68.7 Å Quality: EXCELLENT

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

ABL TYROSINE KINASE

Homo sapiens

UniProt P00519

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 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 64–121 片段:SH3 DOMAIN PEPTIDE P41 × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 3.1;CRYSTALS WITH DIMENSIONS 0.25X0.25X0.25 MM3 WERE OBTAINED AT ROOM TEMPERATURE BY VAPOUR DIFFUSION AGAINST A RESERVOIR CONTAINING 0.1 M CITRIC ACID PH 3.1, 2 M AMMONIUM SULPHATE, 0.2 M SODIUM CHLORIDE, AND 1MM DTT/EDTA. THE HANGING DROP CONTAINED 1:1 RATIO OF RESERVOIR AND PROTEIN-PEPTIDE SOLUTIONS., vapor diffusion 分辨率 1.65 Å R-free 0.266
2 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 C; UniProt 64–121 片段:SH3 DOMAIN PEPTIDE P41 × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 3.1;CRYSTALS WITH DIMENSIONS 0.25X0.25X0.25 MM3 WERE OBTAINED AT ROOM TEMPERATURE BY VAPOUR DIFFUSION AGAINST A RESERVOIR CONTAINING 0.1 M CITRIC ACID PH 3.1, 2 M AMMONIUM SULPHATE, 0.2 M SODIUM CHLORIDE, AND 1MM DTT/EDTA. THE HANGING DROP CONTAINED 1:1 RATIO OF RESERVOIR AND PROTEIN-PEPTIDE SOLUTIONS., vapor diffusion 分辨率 1.65 Å R-free 0.266
3 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 E; UniProt 64–121 片段:SH3 DOMAIN PEPTIDE P41 × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 3.1;CRYSTALS WITH DIMENSIONS 0.25X0.25X0.25 MM3 WERE OBTAINED AT ROOM TEMPERATURE BY VAPOUR DIFFUSION AGAINST A RESERVOIR CONTAINING 0.1 M CITRIC ACID PH 3.1, 2 M AMMONIUM SULPHATE, 0.2 M SODIUM CHLORIDE, AND 1MM DTT/EDTA. THE HANGING DROP CONTAINED 1:1 RATIO OF RESERVOIR AND PROTEIN-PEPTIDE SOLUTIONS., vapor diffusion 分辨率 1.65 Å R-free 0.266
4 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 G; UniProt 64–121 片段:SH3 DOMAIN PEPTIDE P41 × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 3.1;CRYSTALS WITH DIMENSIONS 0.25X0.25X0.25 MM3 WERE OBTAINED AT ROOM TEMPERATURE BY VAPOUR DIFFUSION AGAINST A RESERVOIR CONTAINING 0.1 M CITRIC ACID PH 3.1, 2 M AMMONIUM SULPHATE, 0.2 M SODIUM CHLORIDE, AND 1MM DTT/EDTA. THE HANGING DROP CONTAINED 1:1 RATIO OF RESERVOIR AND PROTEIN-PEPTIDE SOLUTIONS., vapor diffusion 分辨率 1.65 Å R-free 0.266

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 80 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 ABL1_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–58; UniProt 64–121 作者链 C; PDB构建体 1–58; UniProt 64–121 作者链 E; PDB构建体 1–58; UniProt 64–121 作者链 G; PDB构建体 1–58; UniProt 64–121

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 1bbz

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1bbz
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1bbz
沉积日期 deposition_date1998-04-28
结构标题 titleCRYSTAL STRUCTURE OF THE ABL-SH3 DOMAIN COMPLEXED WITH A DESIGNED HIGH-AFFINITY PEPTIDE LIGAND: IMPLICATIONS FOR SH3-LIGAND INTERACTIONS
关键词 keywordsCOMPLEX (TRANSFERASE-PEPTIDE), SIGNAL TRANSDUCTION, SH3 DOMAIN, COMPLEX (TRANSFERASE-PEPTIDE) complex; COMPLEX (TRANSFERASE/PEPTIDE)
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_guinier22.72
回转半径 Rg (电子) rg_electron22.05
零角强度 I(0) i016030800.00
分子量 molecular_weight30024.0 kDa
排除体积 excluded_volume37312 ų
包络体积 envelope_volume45313 ų
水化壳体积 shell_volume17863 ų
包络直径 envelope_diameter69.2
壳层 Rg shell_rg27.94
包络 Rg envelope_rg21.88
形状 Rg shape_rg21.99
总 Rg total_rg22.99
总原子数 total_atoms2120
残基数 n_residues272
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 dmax68.7
Rg (实空间) rg_real22.73
Rg 误差 (实空间) rg_real_error0.44
I(0) (实空间) i0_real1.6030e+07
I(0) 误差 (实空间) i0_real_error2.0960e+05
Rg (倒空间) rg_reciprocal22.73
I(0) (倒空间) i0_reciprocal16030000.0000
解质量估计 total_estimate0.9112
解质量评级 solution_quality EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary19.8
偏度 Skewness skewness0.231
峰度 Kurtosis kurtosis-0.721
角度范围 angular_range— – 0.3500 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha8119000.0000
实空间数据点数 n_real_points67
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.978

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) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_idd1bbza_
类 Class classb — All beta proteins
折叠类型 Fold foldb.34 — SH3-like barrel
超家族 Superfamily superfamilyb.34.2 — SH3-domain
家族 Family familyb.34.2.1 — SH3-domain
结构域编号 domain_idd1bbzc_
类 Class classb — All beta proteins
折叠类型 Fold foldb.34 — SH3-like barrel
超家族 Superfamily superfamilyb.34.2 — SH3-domain
家族 Family familyb.34.2.1 — SH3-domain
结构域编号 domain_idd1bbze_
类 Class classb — All beta proteins
折叠类型 Fold foldb.34 — SH3-like barrel
超家族 Superfamily superfamilyb.34.2 — SH3-domain
家族 Family familyb.34.2.1 — SH3-domain
结构域编号 domain_idd1bbzg_
类 Class classb — All beta proteins
折叠类型 Fold foldb.34 — SH3-like barrel
超家族 Superfamily superfamilyb.34.2 — SH3-domain
家族 Family familyb.34.2.1 — SH3-domain

CATH v4.4 (4 domains)

结构域编号 domain_id1bbzA00
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily40 — SH3 Domains
结构域编号 domain_id1bbzC00
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily40 — SH3 Domains
结构域编号 domain_id1bbzE00
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily40 — SH3 Domains
结构域编号 domain_id1bbzG00
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily40 — SH3 Domains

8. 引用文献 (3)

9. 文件与曲线 (10)