1d0v

CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH ITS REACTION PRODUCTS DETERMINED TO 1.9 A RESOLUTION

Method: X-RAY DIFFRACTION D_max: 76.1 Å Quality: GOOD

▼

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

NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE

物种未注明

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 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 1–356	未记录	RBZ ALPHA-RIBAZOLE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；1.3 NH4H2PO4/(NH4)2HPO4, 1MM 5,6-DIMETHYLBENZIMIDAZOLE, 4 % POLYETHYLENEGLYCOL, AND THEN THE CRYSTALS WERE SOAKED IN 21 MM NICOTINATE MONONUCLEOTIDE IN 1.0 M NAH2PO4/K2HPO4 (PH 6.0), VAPOR DIFFUSION, HANGING DROP	分辨率 1.90 Å R-free 0.249

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 1D0V	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
1D0S CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE : 5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH 5, 6-DIMETHYLBENZIMIDAZOLE 提交 1999-09-14	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 2 DMD 5,6-DIMETHYLBENZIMIDAZOLE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；1.3 M NH4H2PO4/(NH4)2HPO4, 1 MM 5,6-DIMETHYLBENZIMIDAZOLE, 4 % POLYETHYLENEGLYCOL 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP	分辨率 1.90 Å
1JH8 Structural Investigation of the Biosynthesis of Alternative Lower Ligands for Cobamides by Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase (CobT) from Salmonella enterica 提交 2001-06-27	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 4 ADE ADENINE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；1.4 M Ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 1.80 Å R-free 0.256
1JHA Structural Investigation of the Biosynthesis of Alternative Lower Ligands for Cobamides by Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase (CobT) from Salmonella enterica 提交 2001-06-27	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 1–356（356 aa）	未记录	AAM ALPHA-ADENOSINE MONOPHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.00 Å R-free 0.275
1JHM Three-dimensional Structure of CobT in Complex with 5-methylbenzimidazole 提交 2001-06-28	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 4 5MB 5-METHYLBENZIMIDAZOLE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.20 Å R-free 0.302
1JHO Three-dimensional Structure of CobT in Complex with the Reaction Products of 5-methylbenzimidazole and NaMN 提交 2001-06-28	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 1–356（356 aa）	未记录	RMB N1-(5'-PHOSPHO-ALPHA-RIBOSYL)-5-METHYLBENZIMIDAZOLE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.00 Å R-free 0.256
1JHP Three-dimensional Structure of CobT in Complex with 5-methoxybenzimidazole 提交 2001-06-28	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 4 5OB 5-METHOXYBENZIMIDAZOLE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.20 Å R-free 0.295
1JHQ Three-dimensional Structure of CobT in Complex with Reaction Products of 5-methoxybenzimidazole and NaMN 提交 2001-06-28	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 1–356（356 aa）	未记录	PMO N1-(5'-PHOSPHO-ALPHA-RIBOSYL)-5-METHOXYBENZIMIDAZOLE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.00 Å R-free 0.279
1JHR Three-dimensional Structure of CobT in Complex with Reaction Products of 2-hydroxypurine and NaMN 提交 2001-06-28	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 1–356（356 aa）	未记录	NIO NICOTINIC ACID × 2 P2P N7-(5'-PHOSPHO-ALPHA-RIBOSYL)-2-HYDROXYPURINE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.00 Å R-free 0.259
1JHU Three-dimensional Structure of CobT in Complex with p-cresol 提交 2001-06-28	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 4 PCR P-CRESOL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.00 Å R-free 0.284
1JHV Three-dimensional Structure of CobT in Complex with p-cresol and Nicotinate 提交 2001-06-28	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 2 PCR P-CRESOL × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.00 Å R-free 0.274
1JHX Three-dimensional Structure of CobT in Complex with Phenol 提交 2001-06-28	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 4 IPH PHENOL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.00 Å R-free 0.267
1JHY Three-dimensional Structure of CobT in Complex with Phenol and Nicotinate 提交 2001-06-28	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 2 IPH PHENOL × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.00 Å R-free 0.264
1L4B Crystal Structure of CobT in apo state 提交 2002-03-04	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 1.70 Å R-free 0.218
1L4E The crystal structure of CobT complexed with alpha-ribazole-5'-phosphate 提交 2002-03-06	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 1–356（356 aa）	未记录	RBZ ALPHA-RIBAZOLE-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate at pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.00 Å R-free 0.218
1L4F The crystal structure of CobT complexed with 4,5-dimethyl-1,2-phenylenediamine and nicotinate mononucleotide 提交 2002-03-06	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 1–356（356 aa）	未记录	150 4,5-DIMETHYL-1,2-PHENYLENEDIAMINE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.10 Å R-free 0.221
1L4G Crystal Structure of CobT complexed with 4-methylcatechol and nicotinate mononucleotide 提交 2002-03-06	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 1–356（356 aa）	未记录	MCT 4-METHYLCATECHOL × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.10 Å R-free 0.226
1L4H Crystal Structure of CobT complexed with indole and nicotinate mononucleotide 提交 2002-03-06	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 1–356（356 aa）	未记录	IND INDOLE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.10 Å R-free 0.209
1L4K Crystal Structure of CobT complexed with 3,4-dimethylaniline and nicotinate mononucleotide 提交 2002-03-06	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 1–356（356 aa）	未记录	34A 3,4-DIMETHYLANILINE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.20 Å R-free 0.207
1L4L Crystal Structure of CobT complexed with 2,5-dimethylaniline and nicotinate mononucleotide 提交 2002-03-06	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 1–356（356 aa）	未记录	XYD 2,5-DIMETHYLANILINE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.00 Å R-free 0.202
1L4M Crystal Structure of CobT complexed with 2-amino-p-cresol and nicotinate mononucleotide 提交 2002-03-06	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 1–356（356 aa）	未记录	2AC 2-AMINO-P-CRESOL × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.00 Å R-free 0.216
1L4N Crystal Structure of CobT complexed with 2-aminophenol 提交 2002-03-06	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 2 2AF 2-AMINOPHENOL × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.00 Å R-free 0.199
1L5F Crystal Structure of CobT complexed with benzimidazole 提交 2002-03-06	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 4 BZI BENZIMIDAZOLE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 1.90 Å R-free 0.215
1L5K Crystal Structure of CobT complexed with N1-(5'-phosphoribosyl)-benzimidazole and nicotinate 提交 2002-03-07	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 1–356（356 aa）	未记录	1RB 1-ALPHA-D-RIBOFURANOSYL-BENZIMIAZOLE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.00 Å R-free 0.216
1L5L Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)purine and nicotinate 提交 2002-03-07	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 1–356（356 aa）	未记录	7RP 7-ALPHA-D-RIBOFURANOSYL-PURINE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.00 Å R-free 0.197
1L5M Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)-2-aminopurine and nicotinate 提交 2002-03-07	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 1–356（356 aa）	未记录	7RA 7-ALPHA-D-RIBOFURANOSYL-2-AMINOPURINE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 2.00 Å R-free 0.218
1L5N Crystal Structure of CobT complexed with imidazole 提交 2002-03-07	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 1–356（356 aa）	未记录	PO4 PHOSPHATE ION × 2 IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 1.90 Å R-free 0.200
1L5O Crystal Structure of CobT complexed with 3,4-dimethylphenol and nicotinate mononucleotide 提交 2002-03-07	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 1–356（356 aa）	未记录	2MP 3,4-DIMETHYLPHENOL × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	分辨率 1.60 Å R-free 0.199
4KQF Crystal structure of CobT E174A complexed with adenine 提交 2013-05-15	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 × 2 PDB 声明：dimeric	链 A 1–356（356 aa）	突变：E174A	SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 ADE ADENINE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 6；298 K；1.05 M ammonium sulfate, 0.1 M MES, 5% glycerol, pH 6.0, VAPOR DIFFUSION, temperature 298K	分辨率 1.90 Å R-free 0.223
4KQG Crystal structure of CobT E174A complexed with DMB 提交 2013-05-15	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 × 2 PDB 声明：dimeric	链 A 1–356（356 aa）	突变：E174A	PO4 PHOSPHATE ION × 2 DMD 5,6-DIMETHYLBENZIMIDAZOLE × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 6；298 K；10% MEPEG 5000, 0.1 M MES, 0.2 M ammonium sulfate, 5% glycerol, pH 6.0, VAPOR DIFFUSION, temperature 298K	分辨率 1.90 Å R-free 0.225
4KQH Crystal structure of CobT E317A 提交 2013-05-15	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 × 2 PDB 声明：dimeric	链 A 1–356（356 aa）	突变：E317A	SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 6；298 K；20% PEG 1500, 0.1 M MES, 0.05M lithium sulfate, 2.5% ethylene glycol, pH 6.0, VAPOR DIFFUSION, temperature 298K	分辨率 1.90 Å R-free 0.225
4KQI Crystal structure of CobT E317A complexed with its reaction products 提交 2013-05-15	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 × 2 PDB 声明：dimeric	链 A 1–356（356 aa）	突变：E317A	RBZ ALPHA-RIBAZOLE-5'-PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 6；298 K；20% PEG 1500, 0.1 M MES, 0.05 M lithium sulfate, 2.5% ethylene glycol, pH 6.0, VAPOR DIFFUSION, temperature 298K	分辨率 1.40 Å R-free 0.195
4KQJ Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN 提交 2013-05-15	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 × 2 PDB 声明：dimeric	链 A 1–356（356 aa）	突变：S80Y, Q88M, L175M	NCN NICOTINATE MONONUCLEOTIDE × 2 PCR P-CRESOL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 9；298 K；24% MEPEG 5000, 0.1 M CHES, 0.05 M magnesium sulfate, 5 mM p-cresol, 1% DMSO, 5% ethylene glycol, pH 9.0, VAPOR DIFFUSION, temperature 298K	分辨率 1.95 Å R-free 0.223
4KQK Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol 提交 2013-05-15	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 × 2 PDB 声明：dimeric	链 A 1–356（356 aa）链 B 1–356（356 aa）	突变：S80Y, Q88M, L175M 突变：S80Y, Q88M, L175M	SO4 SULFATE ION × 4 PCR P-CRESOL × 2 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 9；298 K；24% MEPEG 5000, 0.1 M CHES, 0.05 M magnesium sulfate, 5 mM p-cresol, 1% DMSO, 20% ethylene glycol, pH 9.0, VAPOR DIFFUSION, temperature 298K	分辨率 1.47 Å R-free 0.195

共 33 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	COBT_SALTY
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–356； UniProt 1–356

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

▼

2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1d0v
沉积日期 deposition_date	1999-09-14
结构标题 title	CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH ITS REACTION PRODUCTS DETERMINED TO 1.9 A RESOLUTION
关键词 keywords	DINUCLEOTIDE-BINDING MOTIF, PHOSPHORIBOSYLTRANSFERASE, TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	20.91 Å
回转半径 Rg (电子) rg_electron	20.16 Å
零角强度 I(0) i0	21320200.00
分子量 molecular_weight	35101.0 kDa
排除体积 excluded_volume	43919 Å³
包络体积 envelope_volume	49020 Å³
水化壳体积 shell_volume	20835 Å³
包络直径 envelope_diameter	76.6 Å
壳层 Rg shell_rg	26.27 Å
包络 Rg envelope_rg	20.76 Å
形状 Rg shape_rg	20.20 Å
总 Rg total_rg	20.83 Å
总原子数 total_atoms	2451
残基数 n_residues	346
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

▼

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

最大尺寸 Dmax dmax	76.1 Å
Rg (实空间) rg_real	20.96 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	2.1320e+07
I(0) 误差 (实空间) i0_real_error	2.9750e+05
Rg (倒空间) rg_reciprocal	20.95 Å
I(0) (倒空间) i0_reciprocal	21320000.0000
解质量估计 total_estimate	0.8276
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	24.3 Å
偏度 Skewness skewness	0.528
峰度 Kurtosis kurtosis	0.148
角度范围 angular_range	— – 0.3800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6661000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.614; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.990

▶

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

▶

6. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
分子量 formula_weight	36645.6 kDa
EC 编号 ec_number	2.4.2.21
来源方法 src_method	nat
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2609

MQTLHALLRDIPAPDAEAMARTQQHIDGLLKPPGSLGRLETLAVQLAGMPGLNGTPQVGEKAVLVMCADHGVWDEGVAVSPKIVTAIQAANMTRGTTGVCVLAAQAGAKVHVIDVGIDAEPIPGVVNMRVARGCGNIAVGPAMSRLQAEALLLEVSRYACDLAQRGVTLFGVGELGMANTTPAAAMVSVFTGSDAKEVVGIGANLPPSRIDNKVDVVRRAIAINQPNPRDGIDVLSKVGGFDLVGMTGVMLGAARCGLPVLLDGFLSYSAALAACQIAPAVRPYLIPSHFSAEKGARIALAHLSMEPYLHMAMRLGEGSGAALAMPIVEAACAMFHNMGELAASNIVLPEGNANAT

实体 2 Entity 2 non-polymer

描述 description	ALPHA-RIBAZOLE-5'-PHOSPHATE
分子量 formula_weight	358.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 non-polymer

描述 description	NICOTINIC ACID
分子量 formula_weight	123.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	158

▼

7. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1d0va_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.39 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
超家族 Superfamily superfamily	c.39.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
家族 Family family	c.39.1.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)

CATH v4.4 (2 domains)

结构域编号 domain_id	1d0vA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1610 — 5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain

结构域编号 domain_id	1d0vA02
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	10210 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	72.100 Å
晶胞边长 b length_b	90.000 Å
晶胞边长 c length_c	47.600 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.1600
R_free r_free	0.2490

fit	/app/data/saxs_computation/d0/1d0v/1d0v.fit
pddf	/app/data/pr_computation/d0/1d0v/1d0v.pr.out
profile	/app/data/saxs_computation/d0/1d0v/1d0v.dat