4m18

Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man)

Method: X-RAY DIFFRACTION Dmax: 138.6 Å Quality: GOOD

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

Pulmonary surfactant-associated protein D

Homo sapiens

UniProt P35247

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 同源多聚体 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 229–375 链 B; UniProt 229–375 链 C; UniProt 229–375 片段:neck and carbohydrate recognition domain (UNP residues 229-375) 突变:D325A/R343V alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 2 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 1 CA CALCIUM ION × 10 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;290 K;Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K 分辨率 3.20 Å R-free 0.222
2 其他组合 同源多聚体 蛋白 × 3 其他聚合物 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 D; UniProt 229–375 链 E; UniProt 229–375 链 F; UniProt 229–375 片段:neck and carbohydrate recognition domain (UNP residues 229-375) 突变:D325A/R343V alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 3 CA CALCIUM ION × 9 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;290 K;Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K 分辨率 3.20 Å R-free 0.222
3 其他组合 同源多聚体 蛋白 × 3 其他聚合物 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 G; UniProt 229–375 链 H; UniProt 229–375 链 I; UniProt 229–375 片段:neck and carbohydrate recognition domain (UNP residues 229-375) 突变:D325A/R343V alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 3 CA CALCIUM ION × 10 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;290 K;Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K 分辨率 3.20 Å R-free 0.222
4 其他组合 同源多聚体 蛋白 × 3 其他聚合物 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 J; UniProt 229–375 链 K; UniProt 229–375 链 L; UniProt 229–375 片段:neck and carbohydrate recognition domain (UNP residues 229-375) 突变:D325A/R343V alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 2 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 1 CA CALCIUM ION × 9 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;290 K;Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K 分辨率 3.20 Å R-free 0.222

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 30 个其他 PDB 条目、33 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 SFTPD_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–147; UniProt 229–375 作者链 B; PDB构建体 1–147; UniProt 229–375 作者链 C; PDB构建体 1–147; UniProt 229–375 作者链 D; PDB构建体 1–147; UniProt 229–375 作者链 E; PDB构建体 1–147; UniProt 229–375 作者链 F; PDB构建体 1–147; UniProt 229–375 作者链 G; PDB构建体 1–147; UniProt 229–375 作者链 H; PDB构建体 1–147; UniProt 229–375 作者链 I; PDB构建体 1–147; UniProt 229–375 作者链 J; PDB构建体 1–147; UniProt 229–375 作者链 K; PDB构建体 1–147; UniProt 229–375 作者链 L; PDB构建体 1–147; UniProt 229–375

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 4m18

P(r) 距离分布 P(r) Distribution

P(r) distribution for 4m18
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id4m18
沉积日期 deposition_date2013-08-02
结构标题 titleCrystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man)
关键词 keywordssurfactant protein, carbohydrate recognition domain, lectin, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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_guinier42.34
回转半径 Rg (电子) rg_electron41.92
零角强度 I(0) i0565952000.00
分子量 molecular_weight192590.0 kDa
排除体积 excluded_volume239670 ų
包络体积 envelope_volume315730 ų
水化壳体积 shell_volume64338 ų
包络直径 envelope_diameter142.0
壳层 Rg shell_rg45.77
包络 Rg envelope_rg41.51
形状 Rg shape_rg41.89
总 Rg total_rg42.20
总原子数 total_atoms13473
残基数 n_residues1721
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 dmax138.6
Rg (实空间) rg_real42.35
Rg 误差 (实空间) rg_real_error1.10
I(0) (实空间) i0_real5.6600e+08
I(0) 误差 (实空间) i0_real_error1.0190e+07
Rg (倒空间) rg_reciprocal42.34
I(0) (倒空间) i0_reciprocal565900000.0000
解质量估计 total_estimate0.8677
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary45.0
偏度 Skewness skewness0.363
峰度 Kurtosis kurtosis-0.331
角度范围 angular_range— – 0.1850 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha38780000.0000
实空间数据点数 n_real_points38
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.665

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) 12 domains

CATH v4.4 (12 domains)

结构域编号 domain_id4m18A00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18B00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18C00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18D00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18E00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18F00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18G00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18H00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18I00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18J00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18K00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4m18L00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A

8. 引用文献 (1)

9. 文件与曲线 (10)