1jhr

Three-dimensional Structure of CobT in Complex with Reaction Products of 2-hydroxypurine and NaMN

Method: X-RAY DIFFRACTION D_max: 70.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase

Salmonella enterica

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–356	Not recorded	NIO NICOTINIC ACID × 2 P2P N7-(5'-PHOSPHO-ALPHA-RIBOSYL)-2-HYDROXYPURINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.259

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1JHR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D0S CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE : 5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH 5, 6-DIMETHYLBENZIMIDAZOLE Deposited 1999-09-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 2 DMD 5,6-DIMETHYLBENZIMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.90 Å
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 Deposited 1999-09-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	RBZ ALPHA-RIBAZOLE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.90 Å R-free 0.249
1JH8 Structural Investigation of the Biosynthesis of Alternative Lower Ligands for Cobamides by Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase (CobT) from Salmonella enterica Deposited 2001-06-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 4 ADE ADENINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；1.4 M Ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 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 Deposited 2001-06-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	AAM ALPHA-ADENOSINE MONOPHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.275
1JHM Three-dimensional Structure of CobT in Complex with 5-methylbenzimidazole Deposited 2001-06-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 4 5MB 5-METHYLBENZIMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.302
1JHO Three-dimensional Structure of CobT in Complex with the Reaction Products of 5-methylbenzimidazole and NaMN Deposited 2001-06-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	RMB N1-(5'-PHOSPHO-ALPHA-RIBOSYL)-5-METHYLBENZIMIDAZOLE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.256
1JHP Three-dimensional Structure of CobT in Complex with 5-methoxybenzimidazole Deposited 2001-06-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 4 5OB 5-METHOXYBENZIMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.295
1JHQ Three-dimensional Structure of CobT in Complex with Reaction Products of 5-methoxybenzimidazole and NaMN Deposited 2001-06-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PMO N1-(5'-PHOSPHO-ALPHA-RIBOSYL)-5-METHOXYBENZIMIDAZOLE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.279
1JHU Three-dimensional Structure of CobT in Complex with p-cresol Deposited 2001-06-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 4 PCR P-CRESOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.284
1JHV Three-dimensional Structure of CobT in Complex with p-cresol and Nicotinate Deposited 2001-06-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 2 PCR P-CRESOL × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.274
1JHX Three-dimensional Structure of CobT in Complex with Phenol Deposited 2001-06-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 4 IPH PHENOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.267
1JHY Three-dimensional Structure of CobT in Complex with Phenol and Nicotinate Deposited 2001-06-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 2 IPH PHENOL × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.264
1L4B Crystal Structure of CobT in apo state Deposited 2002-03-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.70 Å R-free 0.218
1L4E The crystal structure of CobT complexed with alpha-ribazole-5'-phosphate Deposited 2002-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	RBZ ALPHA-RIBAZOLE-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate at pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.00 Å R-free 0.218
1L4F The crystal structure of CobT complexed with 4,5-dimethyl-1,2-phenylenediamine and nicotinate mononucleotide Deposited 2002-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	150 4,5-DIMETHYL-1,2-PHENYLENEDIAMINE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.10 Å R-free 0.221
1L4G Crystal Structure of CobT complexed with 4-methylcatechol and nicotinate mononucleotide Deposited 2002-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	MCT 4-METHYLCATECHOL × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.10 Å R-free 0.226
1L4H Crystal Structure of CobT complexed with indole and nicotinate mononucleotide Deposited 2002-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	IND INDOLE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.10 Å R-free 0.209
1L4K Crystal Structure of CobT complexed with 3,4-dimethylaniline and nicotinate mononucleotide Deposited 2002-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	34A 3,4-DIMETHYLANILINE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.20 Å R-free 0.207
1L4L Crystal Structure of CobT complexed with 2,5-dimethylaniline and nicotinate mononucleotide Deposited 2002-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	XYD 2,5-DIMETHYLANILINE × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.00 Å R-free 0.202
1L4M Crystal Structure of CobT complexed with 2-amino-p-cresol and nicotinate mononucleotide Deposited 2002-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	2AC 2-AMINO-P-CRESOL × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.00 Å R-free 0.216
1L4N Crystal Structure of CobT complexed with 2-aminophenol Deposited 2002-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 2 2AF 2-AMINOPHENOL × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.00 Å R-free 0.199
1L5F Crystal Structure of CobT complexed with benzimidazole Deposited 2002-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 4 BZI BENZIMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.90 Å R-free 0.215
1L5K Crystal Structure of CobT complexed with N1-(5'-phosphoribosyl)-benzimidazole and nicotinate Deposited 2002-03-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	1RB 1-ALPHA-D-RIBOFURANOSYL-BENZIMIAZOLE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.00 Å R-free 0.216
1L5L Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)purine and nicotinate Deposited 2002-03-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	7RP 7-ALPHA-D-RIBOFURANOSYL-PURINE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.00 Å R-free 0.197
1L5M Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)-2-aminopurine and nicotinate Deposited 2002-03-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	7RA 7-ALPHA-D-RIBOFURANOSYL-2-AMINOPURINE-5'-PHOSPHATE × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.00 Å R-free 0.218
1L5N Crystal Structure of CobT complexed with imidazole Deposited 2002-03-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	PO4 PHOSPHATE ION × 2 IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.90 Å R-free 0.200
1L5O Crystal Structure of CobT complexed with 3,4-dimethylphenol and nicotinate mononucleotide Deposited 2002-03-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Not recorded	2MP 3,4-DIMETHYLPHENOL × 2 NCN NICOTINATE MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.60 Å R-free 0.199
4KQF Crystal structure of CobT E174A complexed with adenine Deposited 2013-05-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Mutation：E174A	SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 ADE ADENINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；1.05 M ammonium sulfate, 0.1 M MES, 5% glycerol, pH 6.0, VAPOR DIFFUSION, temperature 298K	Resolution 1.90 Å R-free 0.223
4KQG Crystal structure of CobT E174A complexed with DMB Deposited 2013-05-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Mutation：E174A	PO4 PHOSPHATE ION × 2 DMD 5,6-DIMETHYLBENZIMIDAZOLE × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.90 Å R-free 0.225
4KQH Crystal structure of CobT E317A Deposited 2013-05-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Mutation：E317A	SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.90 Å R-free 0.225
4KQI Crystal structure of CobT E317A complexed with its reaction products Deposited 2013-05-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Mutation：E317A	RBZ ALPHA-RIBAZOLE-5'-PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 2 NIO NICOTINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.40 Å R-free 0.195
4KQJ Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN Deposited 2013-05-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa）	Mutation：S80Y, Q88M, L175M	NCN NICOTINATE MONONUCLEOTIDE × 2 PCR P-CRESOL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.95 Å R-free 0.223
4KQK Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol Deposited 2013-05-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa） Chain B 1–356（356 aa）	Mutation：S80Y, Q88M, L175M Mutation：S80Y, Q88M, L175M	SO4 SULFATE ION × 4 PCR P-CRESOL × 2 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.47 Å R-free 0.195

33 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COBT_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–356； UniProt 1–356

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1jhr
Deposition date deposition_date	2001-06-28
Structure title title	Three-dimensional Structure of CobT in Complex with Reaction Products of 2-hydroxypurine and NaMN
Keywords keywords	CobT, Cobalamin Biosynthesis, Lower ligand, Cobamides, NN:DBI PRT, N1-Alpha-Phosphoribosyltransferase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.48 Å
Radius of gyration Rg (electron density) rg_electron	19.62 Å
Forward intensity I(0) i0	21121600.00
Molecular weight molecular_weight	34711.0 kDa
Excluded volume excluded_volume	43365 Å³
Envelope volume envelope_volume	48036 Å³
Hydration-shell volume shell_volume	20727 Å³
Envelope diameter envelope_diameter	72.7 Å
Shell Rg shell_rg	26.00 Å
Envelope Rg envelope_rg	20.12 Å
Shape Rg shape_rg	19.65 Å
Total Rg total_rg	20.34 Å
Total atoms total_atoms	2423
Residues n_residues	341
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	70.9 Å
Rg (real space) rg_real	20.48 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	2.1120e+07
I(0) uncertainty (real space) i0_real_error	2.9760e+05
Rg (reciprocal space) rg_reciprocal	20.48 Å
I(0) (reciprocal space) i0_reciprocal	21120000.0000
Solution quality estimate total_estimate	0.7815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.428
Kurtosis Kurtosis kurtosis	-0.043
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6558000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.723; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase
Molecular weight formula_weight	36675.6 kDa
EC 编号 ec_number	2.4.2.21
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2569

MQTLHALLRDIPAPDAEAMARTQQHIDGLLKPPGSLGRLETLAVQLAGMPGLNGTPQVGEKAVLVMCADHGVWDEGVAVSPKIVTAIQAANMTRGTTGVCVLAAQAGAKVHVIDVGIDAEPIPGVVNMRVARGCGNIAVGPAMSRLQAEALLLEVSRYTCDLAQRGVTLFGVGELGMANTTPAAAMVSVFTGSDAKEVVGIGANLPPSRIDNKVDVVRRAIAINQPNPRDGIDVLSKVGGFDLVGMTGVMLGAARCGLPVLLDGFLSYSAALAACQIAPAVRPYLIPSHFSAEKGARIALAHLSMEPYLHMAMRLGEGSGAALAMPIVEAACAMFHNMGELAASNIVLPEGNANAT

来源 Source

来源生物 organism	Salmonella enterica
NCBI Class编号 ncbi_taxonomy_id	28901
宿主生物 host_organism	Salmonella enterica

Entity 2 Entity 2 non-polymer

Description description	NICOTINIC ACID
Molecular weight formula_weight	123.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	N7-(5'-PHOSPHO-ALPHA-RIBOSYL)-2-HYDROXYPURINE
Molecular weight formula_weight	348.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1jhra_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.39 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
Superfamily Superfamily superfamily	c.39.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
Family Family family	c.39.1.1 — Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)

CATH v4.4 (2 domains)

Domain ID domain_id	1jhrA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1610 — 5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1
Homologous superfamily homologous superfamily	10 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain

Domain ID domain_id	1jhrA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10210 — Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain

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8. Citations (1)

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Unit-cell length a length_a	71.690 Å
Unit-cell length b length_b	90.150 Å
Unit-cell length c length_c	47.650 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1700
R_free r_free	0.2590

fit	/app/data/saxs_computation/jh/1jhr/1jhr.fit
pddf	/app/data/pr_computation/jh/1jhr/1jhr.pr.out
profile	/app/data/saxs_computation/jh/1jhr/1jhr.dat