5qdd

Crystal structure of BACE complex with BMC020 hydrolyzed

Method: X-RAY DIFFRACTION Dmax: 132.1 Å Quality: GOOD

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

Beta-secretase 1

Homo sapiens

UniProt P56817

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 48–447 未记录 GOL GLYCEROL × 1 E7A (10R,12S)-12-[(1R)-1,2-dihydroxyethyl]-N,N,10-trimethyl-14-oxo-2-oxa-13-azabicyclo[13.3.1]nonadeca-1(19),15,17-triene-17-carboxamide × 1 X-RAY DIFFRACTION X-ray结晶条件:hanging drop;pH 5;292 K;CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE PH 5.0. PROTEIN STOCK WAS BACE MUT46B BATCH XIV 6.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 7-FOLD EXCESS OF BMC020 ADDED FROM A 50MM STOCK SOLUTION IN 90% DMSO, 10% H2O. CRYO-PROTECTANT WAS 1.2M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE, 25%(V/V)GLYCEROL, 2.0% DMSO, 1MM BMC020. 分辨率 2.00 Å R-free 0.187
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 48–447 未记录 GOL GLYCEROL × 1 E7A (10R,12S)-12-[(1R)-1,2-dihydroxyethyl]-N,N,10-trimethyl-14-oxo-2-oxa-13-azabicyclo[13.3.1]nonadeca-1(19),15,17-triene-17-carboxamide × 1 X-RAY DIFFRACTION X-ray结晶条件:hanging drop;pH 5;292 K;CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE PH 5.0. PROTEIN STOCK WAS BACE MUT46B BATCH XIV 6.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 7-FOLD EXCESS OF BMC020 ADDED FROM A 50MM STOCK SOLUTION IN 90% DMSO, 10% H2O. CRYO-PROTECTANT WAS 1.2M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE, 25%(V/V)GLYCEROL, 2.0% DMSO, 1MM BMC020. 分辨率 2.00 Å R-free 0.187
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 48–447 未记录 GOL GLYCEROL × 1 E7A (10R,12S)-12-[(1R)-1,2-dihydroxyethyl]-N,N,10-trimethyl-14-oxo-2-oxa-13-azabicyclo[13.3.1]nonadeca-1(19),15,17-triene-17-carboxamide × 1 X-RAY DIFFRACTION X-ray结晶条件:hanging drop;pH 5;292 K;CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE PH 5.0. PROTEIN STOCK WAS BACE MUT46B BATCH XIV 6.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 7-FOLD EXCESS OF BMC020 ADDED FROM A 50MM STOCK SOLUTION IN 90% DMSO, 10% H2O. CRYO-PROTECTANT WAS 1.2M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE, 25%(V/V)GLYCEROL, 2.0% DMSO, 1MM BMC020. 分辨率 2.00 Å R-free 0.187

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 430 个其他 PDB 条目、734 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 BACE1_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 3–402; UniProt 48–447 作者链 B; PDB构建体 3–402; UniProt 48–447 作者链 C; PDB构建体 3–402; UniProt 48–447

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 5qdd

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id5qdd
沉积日期 deposition_date2017-12-01
结构标题 titleCrystal structure of BACE complex with BMC020 hydrolyzed
关键词 keywordsHydroloase, D3R, BACE, Ligand Docking, Hydrolase; HYDROLASE
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_guinier39.23
回转半径 Rg (电子) rg_electron39.20
零角强度 I(0) i0229886000.00
分子量 molecular_weight125730.0 kDa
排除体积 excluded_volume158130 ų
包络体积 envelope_volume201490 ų
水化壳体积 shell_volume45249 ų
包络直径 envelope_diameter141.0
壳层 Rg shell_rg42.61
包络 Rg envelope_rg38.63
形状 Rg shape_rg39.20
总 Rg total_rg39.43
总原子数 total_atoms8872
残基数 n_residues1112
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 dmax132.1
Rg (实空间) rg_real39.58
Rg 误差 (实空间) rg_real_error1.28
I(0) (实空间) i0_real2.2990e+08
I(0) 误差 (实空间) i0_real_error4.3100e+06
Rg (倒空间) rg_reciprocal39.37
I(0) (倒空间) i0_reciprocal229800000.0000
解质量估计 total_estimate0.8380
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary36.3
偏度 Skewness skewness0.474
峰度 Kurtosis kurtosis-0.446
角度范围 angular_range— – 0.2000 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha61280000.0000
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: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.816; Smooth: 0.633

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) 9 domains

SCOP 2.08 (3 domains)

结构域编号 domain_idd5qdda_
类 Class classb — All beta proteins
折叠类型 Fold foldb.50 — Acid proteases
超家族 Superfamily superfamilyb.50.1 — Acid proteases
家族 Family familyb.50.1.2 — Pepsin-like
结构域编号 domain_idd5qddb_
类 Class classb — All beta proteins
折叠类型 Fold foldb.50 — Acid proteases
超家族 Superfamily superfamilyb.50.1 — Acid proteases
家族 Family familyb.50.1.2 — Pepsin-like
结构域编号 domain_idd5qddc_
类 Class classb — All beta proteins
折叠类型 Fold foldb.50 — Acid proteases
超家族 Superfamily superfamilyb.50.1 — Acid proteases
家族 Family familyb.50.1.2 — Pepsin-like

CATH v4.4 (6 domains)

结构域编号 domain_id5qddA01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily10 — Acid Proteases
结构域编号 domain_id5qddA02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily10 — Acid Proteases
结构域编号 domain_id5qddB01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily10 — Acid Proteases
结构域编号 domain_id5qddB02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily10 — Acid Proteases
结构域编号 domain_id5qddC01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily10 — Acid Proteases
结构域编号 domain_id5qddC02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily10 — Acid Proteases

8. 引用文献 (1)

9. 文件与曲线 (10)