9qvu

Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepI-(1,5)-KdoI ligand

Method: X-RAY DIFFRACTION D_max: 79.1 Å Quality: EXCELLENT

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

Pulmonary surfactant-associated protein D

Homo sapiens

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	蛋白同源多聚体同源多聚体蛋白 × 3 PDB 声明：trimeric（3）与蛋白拷贝数一致	链 A； UniProt 201–375 链 B； UniProt 201–375 链 C； UniProt 201–375	片段：Trimeric neck + carbohydrate recognition domain	CA CALCIUM ION × 9 GMH L-glycero-alpha-D-manno-heptopyranose × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；16% PEG 4000 and 0.1 M Tris pH 8.0	分辨率 1.75 Å R-free 0.206

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。

其他 PDB	相对当前条目 9QVU	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1B08 LUNG SURFACTANT PROTEIN D (SP-D) (FRAGMENT) 提交 1998-11-18	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 218–375（158 aa）片段：TRIMERIC FRAGMENT CONSISTING OF LECTIN DOMAINS AND ALPHA-HELICAL COILED-COIL 链 B 218–375（158 aa）片段：TRIMERIC FRAGMENT CONSISTING OF LECTIN DOMAINS AND ALPHA-HELICAL COILED-COIL 链 C 218–375（158 aa）片段：TRIMERIC FRAGMENT CONSISTING OF LECTIN DOMAINS AND ALPHA-HELICAL COILED-COIL	未记录	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray结晶条件 pH 7；AN EQUAL AMOUNT OF PROTEIN SOLUTION (8 MG/ML PROTEIN IN 10 MM TRIS 140 MM NACL 1MM CACL2 0.02% (W/V) NAN3 PH 7.5) AND PRECIPITANT BUFFER (10-20% (W/V) PEG 20000 IN 100 MM TRIS PH 6-8) WERE MIXED AND VAPOR EQUILIBRATED AGAINST THE LATTER., pH 7.00	分辨率 2.30 Å R-free 0.271
1M7L Solution Structure of the Coiled-Coil Trimerization Domain from Lung Surfactant Protein D 提交 2002-07-22	构建体不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 220–257（38 aa）片段：Trimeric Coiled-Coil Domain 链 B 220–257（38 aa）片段：Trimeric Coiled-Coil Domain 链 C 220–257（38 aa）片段：Trimeric Coiled-Coil Domain	未记录	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 4.4；303 K NMR样品组成 90% H2O/10% D2O	分辨率未提供
1PW9 High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D 提交 2003-07-01	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 199–375（177 aa）片段：Residues 179-355 链 B 199–375（177 aa）片段：Residues 179-355 链 C 199–375（177 aa）片段：Residues 179-355	未记录	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；PEG 4000, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	分辨率 1.60 Å R-free 0.249
1PWB High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D with maltose 提交 2003-07-01	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 199–375（177 aa）片段：recombinant fragment 链 B 199–375（177 aa）片段：recombinant fragment 链 C 199–375（177 aa）片段：recombinant fragment	未记录	CA CALCIUM ION × 9 GLC alpha-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG 10000, Tris, maltose, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	分辨率 1.40 Å R-free 0.228
2GGU crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with maltotriose 提交 2006-03-24	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：trimeric neck and carbohydrate recognition domain 链 B 223–375（153 aa）片段：trimeric neck and carbohydrate recognition domain 链 C 223–375（153 aa）片段：trimeric neck and carbohydrate recognition domain	未记录	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；12% PEG 8000, 150mM NaCl, 10mM CaCl2, 100mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.90 Å R-free 0.248
2GGX Crystal structure of the trimer neck and carbohydrate recognition domain of human surfactant protein D in complex with p-nitrophenyl maltoside 提交 2006-03-24	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：Trimeric neck and carbohydrate recognition domain 链 B 223–375（153 aa）片段：Trimeric neck and carbohydrate recognition domain 链 C 223–375（153 aa）片段：Trimeric neck and carbohydrate recognition domain	未记录	CA CALCIUM ION × 9 NPJ 4-NITROPHENYL 4-O-ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GALACTOPYRANOSIDE × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；12% PEG 8000, 150mM NaCl, 10mM CaCl2, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.90 Å R-free 0.238
2ORJ crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with N-acetyl mannosamine 提交 2007-02-02	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：head and neck domain 链 B 223–375（153 aa）片段：head and neck domain 链 C 223–375（153 aa）片段：head and neck domain	未记录	CA CALCIUM ION × 9 BM3 2-acetamido-2-deoxy-alpha-D-mannopyranose × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150mM NaCl, 10mM CaCl2, 12% PEG 8000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.80 Å R-free 0.205
2ORK crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with inositol-1-phosphate 提交 2007-02-02	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：head and neck domain 链 B 223–375（153 aa）片段：head and neck domain 链 C 223–375（153 aa）片段：head and neck domain	未记录	CA CALCIUM ION × 9 IPD D-MYO-INOSITOL-1-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150mM NaCl, 10mM CaCl2, 12% PEG 8000, 100mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.89 Å R-free 0.226
2OS9 crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with myoinositol 提交 2007-02-05	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：head and neck domain 链 B 223–375（153 aa）片段：head and neck domain 链 C 223–375（153 aa）片段：head and neck domain	未记录	CA CALCIUM ION × 9 INS 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150mM NaCl, 10mM CaCl2, 12% PEG 8000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.70 Å R-free 0.223
2RIA Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose 提交 2007-10-10	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 B 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 C 223–375（153 aa）片段：neck and carbohydrate recognition domain	未记录	CA CALCIUM ION × 9 289 D-glycero-alpha-D-manno-heptopyranose × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.80 Å R-free 0.237
2RIB Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with L-glycero-D-manno-heptose 提交 2007-10-10	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 B 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 C 223–375（153 aa）片段：neck and carbohydrate recognition domain	未记录	CA CALCIUM ION × 9 GMH L-glycero-alpha-D-manno-heptopyranose × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES , PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.80 Å R-free 0.204
2RIC Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with L-glycero-D-manno-heptopyranosyl-(1-3)-L-glycero-D-manno-heptopyranose 提交 2007-10-10	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 B 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 C 223–375（153 aa）片段：neck and carbohydrate recognition domain	未记录	CA CALCIUM ION × 9 GMH L-glycero-alpha-D-manno-heptopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES , PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.80 Å R-free 0.230
2RID Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with Allyl 7-O-carbamoyl-L-glycero-D-manno-heptopyranoside 提交 2007-10-10	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 B 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 C 223–375（153 aa）片段：neck and carbohydrate recognition domain	未记录	CA CALCIUM ION × 9 291 prop-2-en-1-yl 7-O-carbamoyl-L-glycero-alpha-D-manno-heptopyranoside × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.80 Å R-free 0.232
2RIE Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with 2-deoxy-L-glycero-D-manno-heptose 提交 2007-10-10	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 B 223–375（153 aa）片段：neck and carbohydrate recognition domain 链 C 223–375（153 aa）片段：neck and carbohydrate recognition domain	未记录	CA CALCIUM ION × 9 293 2-deoxy-beta-L-galacto-heptopyranose × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.60 Å R-free 0.212
3DBZ human surfactant protein D 提交 2008-06-02	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：Head and Neck Domain, UNP residues 223-375 链 B 223–375（153 aa）片段：Head and Neck Domain, UNP residues 223-375 链 C 223–375（153 aa）片段：Head and Neck Domain, UNP residues 223-375	未记录	CA CALCIUM ION × 9 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150MM NACL, 10MM CACL2, 12% PEG8000, 100MM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.80 Å R-free 0.202
3G81 Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with alpha methyl mannoside 提交 2009-02-11	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：UNP residues 223-375 链 B 223–375（153 aa）片段：UNP residues 223-375 链 C 223–375（153 aa）片段：UNP residues 223-375	未记录	CA CALCIUM ION × 9 MMA methyl alpha-D-mannopyranoside × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150MM NACL, 10MM CACL2, 12% PEG 8000, 100MM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.80 Å R-free 0.200
3G83 Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with alpha 1,2 dimannose. 提交 2009-02-11	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：UNP residues 223-375 链 B 223–375（153 aa）片段：UNP residues 223-375 链 C 223–375（153 aa）片段：UNP residues 223-375	未记录	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150MM NACL, 10MM CACL2, 12% PEG 8000, 100MM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 1.90 Å R-free 0.215
3G84 Crystal structure of the trimeric neck and carbohydrate recognition domain of R343V mutant of human surfactant protein D in complex with alpha 1,2 dimannose. 提交 2009-02-11	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 223–375（153 aa）片段：UNP residues 223-375 链 B 223–375（153 aa）片段：UNP residues 223-375 链 C 223–375（153 aa）片段：UNP residues 223-375	突变：R343V 突变：R343V 突变：R343V	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150MM NACL, 10MM CACL2, 12% PEG 8000, 100MM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	分辨率 2.30 Å R-free 0.191
3IKN Crystal structure of galactose bound trimeric human lung surfactant protein D 提交 2009-08-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 199–375（177 aa）片段：UNP residues 199-375 链 B 199–375（177 aa）片段：UNP residues 199-375 链 C 199–375（177 aa）片段：UNP residues 199-375	突变：P180S 突变：P180S 突变：P180S	CA CALCIUM ION × 10 GAL beta-D-galactopyranose × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.60 Å R-free 0.215
3IKP Crystal structure of inositol phosphate bound trimeric human lung surfactant protein D 提交 2009-08-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 199–375（177 aa）片段：UNP residues 199-375 链 B 199–375（177 aa）片段：UNP residues 199-375 链 C 199–375（177 aa）片段：UNP residues 199-375	突变：P180S 突变：P180S 突变：P180S	CA CALCIUM ION × 10 IPD D-MYO-INOSITOL-1-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.75 Å R-free 0.213
3IKQ Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D 提交 2009-08-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 199–375（177 aa）片段：UNP residues 199-375 链 B 199–375（177 aa）片段：UNP residues 199-375 链 C 199–375（177 aa）片段：UNP residues 199-375	突变：P180S 突变：P180S 突变：P180S	CA CALCIUM ION × 10 MAN alpha-D-mannopyranose × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.25 Å R-free 0.239
3IKR Crystal structure of alpha 1-4 mannobiose bound trimeric human lung surfactant protein D 提交 2009-08-06	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 199–375（177 aa）片段：UNP residues 199-375 链 B 199–375（177 aa）片段：UNP residues 199-375 链 C 199–375（177 aa）片段：UNP residues 199-375	突变：P180S 突变：P180S 突变：P180S	CA CALCIUM ION × 10 MAN alpha-D-mannopyranose × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.65 Å R-free 0.212
4E52 Crystal structure of Haemophilus Eagan 4A polysaccharide bound human lung surfactant protein D 提交 2012-03-13	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 201–375（175 aa）片段：carbohydrate recognition domain 链 B 201–375（175 aa）片段：carbohydrate recognition domain 链 C 201–375（175 aa）片段：carbohydrate recognition domain	未记录	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 4000, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.70 Å R-free 0.210
4M17 Crystal Structure of Surfactant Protein-D D325A/R343V mutant 提交 2013-08-02	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 B 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 C 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375)	突变：D325A/R343V 突变：D325A/R343V 突变：D325A/R343V	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 2.10 Å R-free 0.188
4M17 Crystal Structure of Surfactant Protein-D D325A/R343V mutant 提交 2013-08-02	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 D 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 E 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 F 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375)	突变：D325A/R343V 突变：D325A/R343V 突变：D325A/R343V	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 2.10 Å R-free 0.188
4M17 Crystal Structure of Surfactant Protein-D D325A/R343V mutant 提交 2013-08-02	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 G 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 H 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 I 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375)	突变：D325A/R343V 突变：D325A/R343V 突变：D325A/R343V	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 2.10 Å R-free 0.188
4M17 Crystal Structure of Surfactant Protein-D D325A/R343V mutant 提交 2013-08-02	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 J 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 K 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 L 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375)	突变：D325A/R343V 突变：D325A/R343V 突变：D325A/R343V	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 2.10 Å R-free 0.188
4M18 Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man) 提交 2013-08-02	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 B 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 C 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375)	突变：D325A/R343V 突变：D325A/R343V 突变：D325A/R343V	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
4M18 Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man) 提交 2013-08-02	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 D 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 E 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 F 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375)	突变：D325A/R343V 突变：D325A/R343V 突变：D325A/R343V	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
4M18 Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man) 提交 2013-08-02	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 3 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 G 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 H 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 I 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375)	突变：D325A/R343V 突变：D325A/R343V 突变：D325A/R343V	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
4M18 Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man) 提交 2013-08-02	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 4 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 J 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 K 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375) 链 L 229–375（147 aa）片段：neck and carbohydrate recognition domain (UNP residues 229-375)	突变：D325A/R343V 突变：D325A/R343V 突变：D325A/R343V	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
5OXR Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R7 oligosaccharide 提交 2017-09-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 B 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 C 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain	未记录	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris pH 7.0, 16% PEG 10000	分辨率 1.75 Å R-free 0.196
5OXS Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R5 oligosaccharide 提交 2017-09-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 B 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 C 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain	未记录	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris pH 8.0, 16% PEG 6000	分辨率 1.65 Å R-free 0.187
9QW2 Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepII-HepI-PhosI ligand 提交 2025-04-14	聚集状态不同配体/离子不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 B 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 C 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain	未记录	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；16% PEG 4000 and 0.1 M Tris pH 8.0	分辨率 1.92 Å R-free 0.212
9QW3 Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepIII-HepII-HepI ligand 提交 2025-04-14	聚集状态不同配体/离子不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 B 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 C 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain	未记录	CA CALCIUM ION × 9 A1JBO ~{N}-[4-[2-[(2~{S},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxyethyl]phenyl]-2,2,2-tris(fluoranyl)ethanamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；16% PEG 4000 and 0.1 M Tris pH 8.0	分辨率 1.63 Å R-free 0.199
9QW4 Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic PhosII-HepII-HepI ligand 提交 2025-04-14	配体/离子不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 B 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain 链 C 201–375（175 aa）片段：Trimeric neck + carbohydrate recognition domain	未记录	CA CALCIUM ION × 9 A1JBS [(2~{R},3~{S},4~{R},5~{S},6~{S})-2-[(1~{S})-1,2-bis(oxidanyl)ethyl]-6-[(2~{R},3~{R},4~{S},5~{S},6~{S})-2-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,5-bis(oxidanyl)-6-[2-[4-[2,2,2-tris(fluoranyl)ethanoylamino]phenyl]ethoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate × 1 GMH L-glycero-alpha-D-manno-heptopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；16% PEG 4000 and 0.1 M Tris pH 8.0	分辨率 1.85 Å R-free 0.201

共 30 个其他 PDB 条目、36 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 3–177； UniProt 201–375 作者链 B； PDB构建体 3–177； UniProt 201–375 作者链 C； PDB构建体 3–177； UniProt 201–375

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

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	9qvu
沉积日期 deposition_date	2025-04-12
结构标题 title	Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepI-(1,5)-KdoI ligand
关键词 keywords	;Trimeric recombinant collectin fragment, neck+CRD, alpha-helical coiled coil, carbohydrate recognition domain, lectin, sugar binding protein, surfactant protein ;; SURFACTANT PROTEIN
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	26.62 Å
回转半径 Rg (电子) rg_electron	25.33 Å
零角强度 I(0) i0	43720700.00
分子量 molecular_weight	49989.0 kDa
排除体积 excluded_volume	62019 Å³
包络体积 envelope_volume	74679 Å³
水化壳体积 shell_volume	25618 Å³
包络直径 envelope_diameter	80.8 Å
壳层 Rg shell_rg	31.38 Å
包络 Rg envelope_rg	25.54 Å
形状 Rg shape_rg	25.28 Å
总 Rg total_rg	26.20 Å
总原子数 total_atoms	3501
残基数 n_residues	453
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	79.1 Å
Rg (实空间) rg_real	26.49 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	4.3720e+07
I(0) 误差 (实空间) i0_real_error	6.0200e+05
Rg (倒空间) rg_reciprocal	26.54 Å
I(0) (倒空间) i0_reciprocal	43720000.0000
解质量估计 total_estimate	0.9118
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	39.5 Å
偏度 Skewness skewness	0.028
峰度 Kurtosis kurtosis	-0.780
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15470000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.985

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

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6. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	Pulmonary surfactant-associated protein D
分子量 formula_weight	18835.0 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	3891

GSPGLKGDKGIPGDKGAKGESGLPDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

实体 2 Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

实体 3 Entity 3 non-polymer

描述 description	L-glycero-alpha-D-manno-heptopyranose
分子量 formula_weight	210.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 4 Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	385

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8. 引用文献 (1)

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晶胞边长 a length_a	55.181 Å
晶胞边长 b length_b	106.780 Å
晶胞边长 c length_c	55.469 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.25 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.750 Å
最低分辨率 resolution_low	55.430 Å
R 因子 r_factor	—
R_work r_work	0.1740
R_free r_free	0.2060

fit	/app/data/saxs_computation/qv/9qvu/9qvu.fit
pddf	/app/data/pr_computation/qv/9qvu/9qvu.pr.out
profile	/app/data/saxs_computation/qv/9qvu/9qvu.dat