SAXSdb — 5vmt

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

Glyceraldehyde-3-phosphate dehydrogenase

Neisseria gonorrhoeae

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 × 4 PDB 声明：tetrameric（4）与蛋白拷贝数一致	链 A； UniProt 24–357 链 B； UniProt 24–357 链 C； UniProt 24–357 链 D； UniProt 24–357	片段：residues 24-357	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；NegoA.00617.a.B1.PS38018 at 21.2 mg/mL with 3 mM NAD against JCSG+ screen condition A9 0.2 M ammonium chloride, 25% PEG 3350 supplemented with 20% ethylene glycol and 3 mM NAD as cryoprotectant, crystal tracking ID 284230a9, unique puck ID giy4-10	分辨率 2.50 Å R-free 0.219
2	蛋白同源多聚体同源多聚体蛋白 × 4 PDB 声明：tetrameric（4）与蛋白拷贝数一致	链 E； UniProt 24–357 链 F； UniProt 24–357 链 G； UniProt 24–357 链 H； UniProt 24–357	片段：residues 24-357	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；NegoA.00617.a.B1.PS38018 at 21.2 mg/mL with 3 mM NAD against JCSG+ screen condition A9 0.2 M ammonium chloride, 25% PEG 3350 supplemented with 20% ethylene glycol and 3 mM NAD as cryoprotectant, crystal tracking ID 284230a9, unique puck ID giy4-10	分辨率 2.50 Å R-free 0.219

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 5VMT	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
9Y4U Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form) 提交 2025-09-03	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 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 24–357（334 aa）片段：residues 24-357 链 B 24–357（334 aa）片段：residues 24-357	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；Berkeley D4: 25% (w/v) PEG 3350, 100 mM sodium acetate pH 4.5. 2mM NAD addied prior to crystallization, plate 20205 well D4 drop 3 , Puck: PSL2003, Cryo: 80% crystallant + 20% PEG 200	分辨率 1.90 Å R-free 0.214
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) 提交 2025-11-18	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 × 4 PDB 声明：tetrameric	链 A 24–357（334 aa）片段：residues 24-357 链 B 24–357（334 aa）片段：residues 24-357 链 C 24–357（334 aa）片段：residues 24-357 链 D 24–357（334 aa）片段：residues 24-357	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	分辨率 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) 提交 2025-11-18	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 × 4 PDB 声明：tetrameric	链 E 24–357（334 aa）片段：residues 24-357 链 F 24–357（334 aa）片段：residues 24-357 链 G 24–357（334 aa）片段：residues 24-357 链 H 24–357（334 aa）片段：residues 24-357	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	分辨率 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) 提交 2025-11-18	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 × 4 PDB 声明：tetrameric	链 I 24–357（334 aa）片段：residues 24-357 链 J 24–357（334 aa）片段：residues 24-357 链 K 24–357（334 aa）片段：residues 24-357 链 L 24–357（334 aa）片段：residues 24-357	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	分辨率 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) 提交 2025-11-18	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 × 4 PDB 声明：tetrameric	链 M 24–357（334 aa）片段：residues 24-357 链 N 24–357（334 aa）片段：residues 24-357 链 O 24–357（334 aa）片段：residues 24-357 链 P 24–357（334 aa）片段：residues 24-357	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	分辨率 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) 提交 2025-11-18	配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 Q 24–357（334 aa）片段：residues 24-357 链 R 24–357（334 aa）片段：residues 24-357 链 S 24–357（334 aa）片段：residues 24-357 链 T 24–357（334 aa）片段：residues 24-357	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	分辨率 2.30 Å R-free 0.232
9Z9C Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form) 提交 2025-11-18	配体/离子不同实验环境不同结构质量不同	Assembly 6 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 U 24–357（334 aa）片段：residues 24-357 链 V 24–357（334 aa）片段：residues 24-357 链 W 24–357（334 aa）片段：residues 24-357 链 X 24–357（334 aa）片段：residues 24-357	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200	分辨率 2.30 Å R-free 0.232
9ZAG Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE 提交 2025-11-19	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 × 4 PDB 声明：tetrameric	链 A 24–357（334 aa）链 B 24–357（334 aa）链 C 24–357（334 aa）链 D 24–357（334 aa）	未记录	G3H GLYCERALDEHYDE-3-PHOSPHATE × 4 PEG DI(HYDROXYETHYL)ETHER × 5 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 NA SODIUM ION × 4 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Berkeley H9: 25% PEG 4000, 0.10M HEPES pH 7.5, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD and G3H, plate 20061 H9 drop 1, Puck: PSL-2203, Cryo: 80% crystallant + 20% PEG 200	分辨率 1.91 Å R-free 0.187
9ZAG Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE 提交 2025-11-19	构建体不同配体/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 × 4 PDB 声明：tetrameric	链 E 24–357（334 aa）链 F 24–357（334 aa）链 G 24–357（334 aa）链 H 24–357（334 aa）	未记录	G3H GLYCERALDEHYDE-3-PHOSPHATE × 4 PEG DI(HYDROXYETHYL)ETHER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 NA SODIUM ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Berkeley H9: 25% PEG 4000, 0.10M HEPES pH 7.5, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD and G3H, plate 20061 H9 drop 1, Puck: PSL-2203, Cryo: 80% crystallant + 20% PEG 200	分辨率 1.91 Å R-free 0.187
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) 提交 2025-11-19	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 × 4 PDB 声明：tetrameric	链 A 24–357（334 aa）链 B 24–357（334 aa）链 C 24–357（334 aa）链 D 24–357（334 aa）	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 3 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	分辨率 3.09 Å R-free 0.234
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) 提交 2025-11-19	构建体不同配体/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 × 4 PDB 声明：tetrameric	链 E 24–357（334 aa）链 F 24–357（334 aa）链 G 24–357（334 aa）链 H 24–357（334 aa）	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	分辨率 3.09 Å R-free 0.234
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) 提交 2025-11-19	构建体不同配体/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 × 4 PDB 声明：tetrameric	链 I 24–357（334 aa）链 J 24–357（334 aa）链 K 24–357（334 aa）链 L 24–357（334 aa）	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	分辨率 3.09 Å R-free 0.234
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) 提交 2025-11-19	构建体不同配体/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 × 4 PDB 声明：tetrameric	链 M 24–357（334 aa）链 N 24–357（334 aa）链 O 24–357（334 aa）链 P 24–357（334 aa）	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	分辨率 3.09 Å R-free 0.234
9ZAO Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2) 提交 2025-11-19	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白同源多聚体同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 Q 24–357（334 aa）链 R 24–357（334 aa）链 S 24–357（334 aa）链 T 24–357（334 aa）	未记录	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct	分辨率 3.09 Å R-free 0.234

共 4 个其他 PDB 条目、14 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	B4RPP8_NEIG2
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 9–342； UniProt 24–357 作者链 B； PDB构建体 9–342； UniProt 24–357 作者链 C； PDB构建体 9–342； UniProt 24–357 作者链 D； PDB构建体 9–342； UniProt 24–357 作者链 E； PDB构建体 9–342； UniProt 24–357 作者链 F； PDB构建体 9–342； UniProt 24–357 作者链 G； PDB构建体 9–342； UniProt 24–357 作者链 H； PDB构建体 9–342； UniProt 24–357

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。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	5vmt
沉积日期 deposition_date	2017-04-28
结构标题 title	Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae bound to NAD
关键词 keywords	;NIAID, structural genomics, co-factor, glycolysis, Seattle Structural Genomics Center for Infectious Disease, SSGCID, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	47.77 Å
回转半径 Rg (电子) rg_electron	47.86 Å
零角强度 I(0) i0	1174200000.00
分子量 molecular_weight	275920.0 kDa
排除体积 excluded_volume	341480 Å³
包络体积 envelope_volume	445410 Å³
水化壳体积 shell_volume	76634 Å³
包络直径 envelope_diameter	166.1 Å
壳层 Rg shell_rg	52.63 Å
包络 Rg envelope_rg	47.09 Å
形状 Rg shape_rg	47.89 Å
总 Rg total_rg	47.91 Å
总原子数 total_atoms	19374
残基数 n_residues	2616
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	163.8 Å
Rg (实空间) rg_real	47.97 Å
Rg 误差 (实空间) rg_real_error	1.54 Å
I(0) (实空间) i0_real	1.1740e+09
I(0) 误差 (实空间) i0_real_error	1.9170e+07
Rg (倒空间) rg_reciprocal	47.78 Å
I(0) (倒空间) i0_reciprocal	1174000000.0000
解质量估计 total_estimate	0.8623
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	49.6 Å
偏度 Skewness skewness	0.398
峰度 Kurtosis kurtosis	-0.490
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	107400000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.799

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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	Glyceraldehyde-3-phosphate dehydrogenase
分子量 formula_weight	36829.8 kDa
EC 编号 ec_number	1.2.1.-
来源方法 src_method	man
拷贝数 entity_count	8

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	20034

MAHHHHHHMSIKVAINGFGRIGRLALRQIEKAHGIEVAAVNDLTPAEMLLHLFKYDSTQGRFQGTAELKDDAIVVNGREIKVFANPNPEELPWGELGVDVVLECTGFFTNKTKAEAHIRAGARKVVISAPGGNDVKTVVYGVNQDILDGSETVISAASCTTNCLAPMAAVLQKEFGVVEGLMTTIHAYTGDQNTLDAPHRKGDLRRARAAALNIVPNSTGAAKAIGLVIPELNGKLDGSAQRVPVATGSLTELVSVLERPATKEEINAAMKAASSESYGYNEDQIVSSDVVGIEYGSLFDATQTRVMTVGGKQLVKTVAWYDNEMSYTCQLVRTLEYFAGKI

来源 Source

来源生物 organism	Neisseria gonorrhoeae
NCBI 分类编号 ncbi_taxonomy_id	521006
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

实体 3 Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	646

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7. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	5vmtA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	5vmtB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	5vmtC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	5vmtD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	5vmtE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	5vmtF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	5vmtG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	5vmtH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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8. 引用文献 (1)

▶

晶胞边长 a length_a	142.450 Å
晶胞边长 b length_b	132.100 Å
晶胞边长 c length_c	156.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.56 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	32

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	45.485 Å
R 因子 r_factor	0.1661
R_work r_work	0.1650
R_free r_free	0.2190

fit	/app/data/saxs_computation/vm/5vmt/5vmt.fit
pddf	/app/data/pr_computation/vm/5vmt/5vmt.pr.out
profile	/app/data/saxs_computation/vm/5vmt/5vmt.dat

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae bound to NAD

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

Glyceraldehyde-3-phosphate dehydrogenase

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