1vg9

The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein

Method: X-RAY DIFFRACTION D_max: 206.0 Å Quality: REASONABLE

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

Rab proteins geranylgeranyltransferase component A 1

Rattus norvegicus

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 1–650	突变：K231Q, K462R, T473A, A483G	Ras-related protein Rab-7 × 1 （P09527） MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.50 Å R-free 0.250
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 1–650	突变：K231Q, K462R, T473A, A483G	Ras-related protein Rab-7 × 1 （P09527） MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.50 Å R-free 0.250
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 1–650	突变：K231Q, K462R, T473A, A483G	Ras-related protein Rab-7 × 1 （P09527） MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.50 Å R-free 0.250
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 1–650	突变：K231Q, K462R, T473A, A483G	Ras-related protein Rab-7 × 1 （P09527） MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.50 Å R-free 0.250

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 1VG9	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
1LTX Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid 提交 2002-05-21	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 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 R 1–650（650 aa）	突变：A473T, G483A, Q231K	ZN ZINC ION × 1 CL CHLORIDE ION × 1 FAR FARNESYL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；20% PEG 3350, 100mM KSCN, 100mM Namalonate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	分辨率 2.70 Å R-free 0.272
1VG0 The crystal structures of the REP-1 protein in complex with monoprenylated Rab7 protein 提交 2004-04-22	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 1–650（650 aa）	突变：K231Q, K462R, T473A, A483G	CL CHLORIDE ION × 1 GER GERAN-8-YL GERAN × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 3350, 0.4M diAmmonium Tartrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.20 Å R-free 0.233

共 2 个其他 PDB 条目、2 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	RAE1_RAT
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–650； UniProt 1–650 作者链 C； PDB构建体 1–650； UniProt 1–650 作者链 E； PDB构建体 1–650； UniProt 1–650 作者链 G； PDB构建体 1–650； UniProt 1–650

Ras-related protein Rab-7

Rattus norvegicus

UniProt P09527

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 B； UniProt 1–185	片段：GTPase domain	Rab proteins geranylgeranyltransferase component A 1 × 1 （P37727） MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.50 Å R-free 0.250
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 D； UniProt 1–185	片段：GTPase domain	Rab proteins geranylgeranyltransferase component A 1 × 1 （P37727） MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.50 Å R-free 0.250
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 F； UniProt 1–185	片段：GTPase domain	Rab proteins geranylgeranyltransferase component A 1 × 1 （P37727） MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.50 Å R-free 0.250
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 H； UniProt 1–185	片段：GTPase domain	Rab proteins geranylgeranyltransferase component A 1 × 1 （P37727） MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 2000 MME, 0.4M Potassium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.50 Å R-free 0.250

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 1VG9	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
1VG0 The crystal structures of the REP-1 protein in complex with monoprenylated Rab7 protein 提交 2004-04-22	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 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 B 1–207（207 aa）	未记录	CL CHLORIDE ION × 1 GER GERAN-8-YL GERAN × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；23% PEG 3350, 0.4M diAmmonium Tartrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.20 Å R-free 0.233
1VG1 GDP-Bound Rab7 提交 2004-04-22	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–185（185 aa）片段：Gtpase Domain	未记录	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；25% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.90 Å R-free 0.247
1VG8 GPPNHP-Bound Rab7 提交 2004-04-23	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–207（207 aa）	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；24% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.70 Å R-free 0.224
1VG8 GPPNHP-Bound Rab7 提交 2004-04-23	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 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 1–207（207 aa）	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；24% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.70 Å R-free 0.224
1VG8 GPPNHP-Bound Rab7 提交 2004-04-23	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 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 1–207（207 aa）	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；24% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.70 Å R-free 0.224
1VG8 GPPNHP-Bound Rab7 提交 2004-04-23	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 4 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 D 1–207（207 aa）	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；24% PEG 3350, 0.25M Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.70 Å R-free 0.224

共 3 个其他 PDB 条目、6 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	RAB7_RAT
Isoform	—
PDB实体	2
链与序列区间	作者链 B； PDB构建体 1–185； UniProt 1–185 作者链 D； PDB构建体 1–185； UniProt 1–185 作者链 F； PDB构建体 1–185； UniProt 1–185 作者链 H； PDB构建体 1–185； UniProt 1–185

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	1vg9
沉积日期 deposition_date	2004-04-23
结构标题 title	The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein
关键词 keywords	RAB PRENYLATION, POST-TRANSLATIONAL MODIFICATION, PROTEIN BINDING-PROTEIN TRANSPORT COMPLEX; PROTEIN BINDING/PROTEIN TRANSPORT
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	72.26 Å
回转半径 Rg (电子) rg_electron	72.82 Å
零角强度 I(0) i0	1329240000.00
分子量 molecular_weight	307440.0 kDa
排除体积 excluded_volume	383840 Å³
包络体积 envelope_volume	614990 Å³
水化壳体积 shell_volume	70687 Å³
包络直径 envelope_diameter	228.6 Å
壳层 Rg shell_rg	72.74 Å
包络 Rg envelope_rg	69.73 Å
形状 Rg shape_rg	72.82 Å
总 Rg total_rg	72.79 Å
总原子数 total_atoms	21562
残基数 n_residues	2688
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	206.0 Å
Rg (实空间) rg_real	72.68 Å
Rg 误差 (实空间) rg_real_error	1.48 Å
I(0) (实空间) i0_real	1.3280e+09
I(0) 误差 (实空间) i0_real_error	2.5050e+07
Rg (倒空间) rg_reciprocal	69.83 Å
I(0) (倒空间) i0_reciprocal	1321000000.0000
解质量估计 total_estimate	0.6593
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	46.8 Å
偏度 Skewness skewness	0.344
峰度 Kurtosis kurtosis	-1.095
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0060
最高正则化参数 α highest_alpha	66120000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.335; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.563; Smooth: 0.000

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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 (7)

实体 1 Entity 1 polymer

描述 description	Rab proteins geranylgeranyltransferase component A 1
分子量 formula_weight	72622.2 kDa
突变 mutation	K231Q, K462R, T473A, A483G
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G
原子数 atom_count	22604

MADNLPSDFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENNDVVTENSMWQEQILENEEAIPLSSKDKTIQHVEVFCYASQDLHKDVEEAGALQKNHASVTSAQSAEAAEAAETSCLPTAVEPLSMGSCEIPAEQSQCPGPESSPEVNDAEATGKKENSDAKSSTEEPSENVPKVQDNTETPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGTVEQVPCSRADVFNSKQLTMVEKRMLMKFLTFCVEYEEHPDEYRAYEGTTFSEYLKTQKLTPNLQYFVLHSIAMTSETTSCTVDGLKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAVIDQFGQRIISKHFIIEDSYLSENTCSRVQYRQISRAVLITDGSVLRTDADQQVSILTVPAEEPGSFAVRVIELCSSTMTCMKGTYLVHLTCMSSKTAREDLERVVQKLFTPYTEIEAENEQVEKPRLLWALYFNMRDSSDISRDCYNDLPSNVYVCSGPDSGLGNDNAVKQAETLFQQICPNEDFCPAPPNPEDIVLDGDSSQQEVPESSVTPETNSETPKESTVLGNPEEPSE

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Spodoptera frugiperda

实体 2 Entity 2 polymer

描述 description	Ras-related protein Rab-7
分子量 formula_weight	21121.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H

MTSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNE

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

实体 3 Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 4 Entity 4 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 5 Entity 5 non-polymer

描述 description	GUANOSINE-5'-DIPHOSPHATE
分子量 formula_weight	443.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 6 Entity 6 non-polymer

描述 description	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
分子量 formula_weight	326.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 7 Entity 7 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	1042

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7. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1vg9a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.3 — GDI-like N domain

结构域编号 domain_id	d1vg9a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.6 — GDI-like

结构域编号 domain_id	d1vg9b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1vg9c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.3 — GDI-like N domain

结构域编号 domain_id	d1vg9c2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.6 — GDI-like

结构域编号 domain_id	d1vg9d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1vg9e1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.3 — GDI-like N domain

结构域编号 domain_id	d1vg9e2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.6 — GDI-like

结构域编号 domain_id	d1vg9f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1vg9g1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.3 — GDI-like N domain

结构域编号 domain_id	d1vg9g2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.6 — GDI-like

结构域编号 domain_id	d1vg9h_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

CATH v4.4 (16 domains)

结构域编号 domain_id	1vg9A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1vg9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 2

结构域编号 domain_id	1vg9A03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1vg9B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1vg9C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1vg9C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 2

结构域编号 domain_id	1vg9C03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1vg9D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1vg9E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1vg9E02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 2

结构域编号 domain_id	1vg9E03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1vg9F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1vg9G01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	50 — FAD/NAD(P)-binding domain
同源超家族 H-superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

结构域编号 domain_id	1vg9G02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	519 — Guanine Nucleotide Dissociation Inhibitor; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 2

结构域编号 domain_id	1vg9G03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

结构域编号 domain_id	1vg9H00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	66.392 Å
晶胞边长 b length_b	144.691 Å
晶胞边长 c length_c	200.086 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.13 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.500 Å
最低分辨率 resolution_low	19.420 Å
R 因子 r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2500

The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein

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

Rab proteins geranylgeranyltransferase component A 1

当前结构中的状态

数据库中的同蛋白其他状态

Ras-related protein Rab-7

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

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

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

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (7)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 polymer

聚合物 Polymer

来源 Source

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 non-polymer

实体 7 Entity 7 water

7. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

CATH v4.4 (16 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/vg/1vg9/1vg9.fit
pddf	/app/data/pr_computation/vg/1vg9/1vg9.pr.out
profile	/app/data/saxs_computation/vg/1vg9/1vg9.dat