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4bnp

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate and magnesium(II)

Method: X-RAY DIFFRACTION Dmax: 76.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ISOCITRATE DEHYDROGENASE [NADP]

ESCHERICHIA COLI

UniProt P08200

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 1–416 Mutation：YES ICT ISOCITRIC ACID × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.8；A SOLUTION OF THE LYS100MET MUTANT (20 MG/ML PROTEIN IN 0.9 MM CITRIC ACID, 3.5 MM NA2HPO4 PH 6.0, 100 MM NACL, 0.02% NAN3 AND 2 MM DTT) WAS MIXED 1:1 WITH A CRYSTALLIZATION SOLUTION (1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4, 0.1 M NACL AND 0.2 M DTT AT PH 5.8) AND 2 UL DROPS EQUILIBRATED AGAINST 500 UL OF THE CRYSTALLIZATION SOLUTION. TETRAGONAL BIPYRAMIDAL CRYSTALS, 300 UM X 150 UM X 75 UM, DEVELOPED WITHIN 5 DAYS. Resolution 2.00 Å R-free 0.192

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 4BNP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AI2 ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND CALCIUM (FLASH-COOLED) Deposited 1997-04-30 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 1–416（416 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ICA ISOCITRATE CALCIUM COMPLEX × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 1.90 Å R-free 0.215
1AI3 ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES Deposited 1997-04-30 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 1–416（416 aa）
Not recorded NDO NICOTINAMIDE-(6-DEAMINO-6-HYDROXY-ADENINE)-DINUCLEOTIDE PHOSPHATE × 2 ICT ISOCITRIC ACID × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 1.90 Å R-free 0.220
1BL5 ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE STRUCTURE OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION Deposited 1998-07-23 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 3–416（414 aa）
Not recorded MG MAGNESIUM ION × 2 AKG 2-OXOGLUTARIC ACID × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.50 Å R-free 0.271
1CW1 CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE MUTANT K230M BOUND TO ISOCITRATE AND MN2+ Deposited 1999-08-25 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 1–416（416 aa）
Mutation：K230M MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；AMMONIUM SULFATE, DTT, NAN3, MN-ISOCITRATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.10 Å R-free 0.233
1CW4 CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ALPHA-KETOGLUTARATE Deposited 1999-08-25 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 1–416（416 aa）
Mutation：K230M MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 2 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；AMMONIUM SULFATE, DTT, NAN3, MN-ALPHA-KETOGLUTARATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.10 Å R-free 0.226
1CW7 LOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG-ISOCITRATE Deposited 1999-08-25 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–416（416 aa）
Not recorded MG MAGNESIUM ION × 2 SO4 SULFATE ION × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；MG-ISOCITRATE, AMMONIUM SULFATE, DTT, NAN3, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.60 Å R-free 0.226
1GRO REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115 Deposited 1995-10-12 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 1–416（416 aa）
Mutation：S113E, N115L MG MAGNESIUM ION × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1GRP REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115 Deposited 1995-10-12 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 1–416（416 aa）
Mutation：N115L MG MAGNESIUM ION × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1HJ6 ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH ISOPROPYLMALATE, NADP+ AND MAGNESIUM (FLASH-COOLED) Deposited 2001-01-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–416（416 aa）
Mutation：YES GOL GLYCEROL × 4 IPM 3-ISOPROPYLMALIC ACID × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；34-44% (NH4)2SO4, 35MM NA2HPO4, 9 MM CITRIC ACID, 100 MM NACL, 0.2 MM DTT, PH 5.4
Resolution 2.00 Å R-free 0.246
1IDC ISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE INTERMEDIATE COMPLEX DETERMINED BY LAUE CRYSTALLOGRAPHY Deposited 1995-01-18 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 1–416（416 aa）
Mutation：K230M MG MAGNESIUM ION × 2 OXS 2-OXALOSUCCINIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1IDD ISOCITRATE DEHYDROGENASE Y160F MUTANT APO ENZYME Deposited 1995-01-18 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 1–416（416 aa）
Mutation：Y160F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions DATA WAS COLLECTED FROM TWO SEPARATE CRYSTALS AND MERGED TOGETHER WITH PROTSYS. THE MERGING R VALUE GIVEN ABOVE IS CRYSTAL TO CRYSTAL. THE MERGING R VALUE FOR INDIVIDUAL CRYSTALS IS 0.064, 0.061
Resolution 2.50 Å R-free 0.246
1IDE ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE COMPLEX (LAUE DETERMINATION) Deposited 1995-01-18 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 1–416（416 aa）
Mutation：Y160F MG MAGNESIUM ION × 2 ICT ISOCITRIC ACID × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1IDF ISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME Deposited 1995-01-18 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 1–416（416 aa）
Mutation：K230M No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.262
1IKA STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE Deposited 1993-06-15 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 1–416（416 aa）
Not recorded CA CALCIUM ION × 2 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1ISO ISOCITRATE DEHYDROGENASE: STRUCTURE OF AN ENGINEERED NADP+--> NAD+ SPECIFICITY-REVERSAL MUTANT Deposited 1996-03-01 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 1–416（416 aa）
Mutation：C201M, C332Y, K344D, Y345I, V351A, Y391K, R395S SO4 SULFATE ION × 6 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.8；pH 5.8
Resolution 1.90 Å R-free 0.218
1P8F A four location model to explain the stereospecificity of proteins. Deposited 2003-05-07 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 1–416（416 aa） Fragment：Full Length
Not recorded SO4 SULFATE ION × 2 MG MAGNESIUM ION × 2 ICT ISOCITRIC ACID × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；IDH, stored in metal-free final buffer, was diluted to 25, 30, 35 and 40 mg/ml using metal-free 2X buffer; (70mM Na2HPO4 , 18 mM citric acid, 200 mM NaCl, 0.4 mM DTT, pH 5.4). and was crystallized from hanging drops using 5 l each of these IDH solutions and 5 l each of 34, 36, 38, 40, 42, and 44 % (NH4)2SO4 solutions in crystallization buffer (35mM Na2HPO4 , 9 mM citric acid, 100 mM NaCl, 0.2 mM DTT at pH 6.1, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Resolution 1.85 Å R-free 0.225
1PB1 A four location model to explain the stereospecificity of proteins. Deposited 2003-05-14 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 1–416（416 aa）
Not recorded SO4 SULFATE ION × 2 ICT ISOCITRIC ACID × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；IDH, stored in metal-free final buffer, was diluted to 25, 30, 35 and 40 mg/ml using metal-free 2X buffer; (70mM Na2HPO4 , 18 mM citric acid, 200 mM NaCl, 0.4 mM DTT, pH 5.4). and was crystallized from hanging drops using 5 l each of these IDH solutions and 5 l each of 34, 36, 38, 40, 42, and 44 % (NH4)2SO4 solutions in crystallization buffer (35mM Na2HPO4 , 9 mM citric acid, 100 mM NaCl, 0.2 mM DTT at pH 5.4). , pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Resolution 1.70 Å R-free 0.211
1PB3 Sites of binding and orientation in a four location model for protein stereospecificity. Deposited 2003-05-14 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 1–416（416 aa）
Not recorded SO4 SULFATE ION × 4 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；IDH, stored in metal-free final buffer, was diluted to 25, 30, 35 and 40 mg/ml using metal-free 2X buffer; (70mM Na2HPO4 , 18 mM citric acid, 200 mM NaCl, 0.4 mM DTT, pH 5.4). and was crystallized from hanging drops using 5 l each of these IDH solutions and 5 l each of 34, 36, 38, 40, 42, and 44 % (NH4)2SO4 solutions in crystallization buffer (35mM Na2HPO4 , 9 mM citric acid, 100 mM NaCl, 0.2 mM DTT at pH 5.4). , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Resolution 1.70 Å R-free 0.216
1SJS ACCESS TO PHOSPHORYLATION IN ISOCITRATE DEHYDROGENASE MAY OCCUR BY DOMAIN SHIFTING Deposited 1997-07-08 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 1–416（416 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；pH 7.4
Resolution 2.42 Å R-free 0.230
3ICD STRUCTURE OF A BACTERIAL ENZYME REGULATED BY PHOSPHORYLATION, ISOCITRATE DEHYDROGENASE Deposited 1989-12-28 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 1–416（416 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
3LCB The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli. Deposited 2010-01-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–416（416 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；25% PEG 300, 0.1M MES, 0.05M magnesium chloride, 0.002M DTT,10% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å R-free 0.222
3LCB The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli. Deposited 2010-01-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–416（416 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；25% PEG 300, 0.1M MES, 0.05M magnesium chloride, 0.002M DTT,10% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å R-free 0.222
3LCB The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli. Deposited 2010-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–416（416 aa）
Chain D 1–416（416 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；25% PEG 300, 0.1M MES, 0.05M magnesium chloride, 0.002M DTT,10% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å R-free 0.222
4AJ3 3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and NADP - The pseudo-Michaelis complex Deposited 2012-02-15 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 1–416（416 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ICT ISOCITRIC ACID × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.8, 0.1 M NACL AND 0.2 M DTT
Resolution 1.90 Å R-free 0.224
4AJA 3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and thioNADP Deposited 2012-02-16 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 1–416（416 aa）
Not recorded TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ICT ISOCITRIC ACID × 2 CA CALCIUM ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.8, 0.1 M NACL AND 0.2 M DTT
Resolution 1.80 Å R-free 0.204
4AJB 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with Isocitrate, magnesium(II) and thioNADP Deposited 2012-02-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–416（416 aa）
Mutation：YES TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ICT ISOCITRIC ACID × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 1.85M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.2, 0.1 M NACL AND 0.2 M DTT
Resolution 1.90 Å R-free 0.180
4AJR 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, magnesium(II) and NADPH - The product complex Deposited 2012-02-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–416（416 aa）
Mutation：YES NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 AKG 2-OXOGLUTARIC ACID × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.2, 0.1 M NACL AND 0.2 M DTT
Resolution 2.69 Å R-free 0.209
4AJS 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate, magnesium(II), Adenosine 2',5'-biphosphate and ribosylnicotinamide-5'-phosphate Deposited 2012-02-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–416（416 aa）
Mutation：YES A2P ADENOSINE-2'-5'-DIPHOSPHATE × 2 ICT ISOCITRIC ACID × 2 MG MAGNESIUM ION × 2 NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.2, 0.1 M NACL AND 0.2 M DTT.
Resolution 1.80 Å R-free 0.192
4ICD REGULATION OF ISOCITRATE DEHYDROGENASE BY PHOSPHORYLATION INVOLVES NO LONG-RANGE CONFORMATIONAL CHANGE IN THE FREE ENZYME Deposited 1989-12-28 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 1–416（416 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
4P69 Acek (D477A) ICDH complex Deposited 2014-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–416（415 aa）
Chain D 2–416（415 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2mM DTT, 10% glycerol, 0.1M MES pH 6.0, 25%~30% PEG 300
Resolution 3.30 Å R-free 0.247
5ICD REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE Deposited 1990-05-30 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 1–416（416 aa）
Not recorded MG MAGNESIUM ION × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
6ICD REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE Deposited 1990-05-30 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 1–416（416 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
7ICD REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE Deposited 1990-05-30 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 1–416（416 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
8ICD REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE Deposited 1990-05-30 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 1–416（416 aa）
Not recorded MG MAGNESIUM ION × 2 ICT ISOCITRIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
9ICD CATALYTIC MECHANISM OF NADP+-DEPENDENT ISOCITRATE DEHYDROGENASE: IMPLICATIONS FROM THE STRUCTURES OF MAGNESIUM-ISOCITRATE AND NADP+ COMPLEXES Deposited 1991-07-29 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 1–416（416 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å

33 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IDH_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–416； UniProt 1–416

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

SAXS profile for 4bnp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4bnp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4bnp
Deposition date deposition_date2013-05-16
Structure title title3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate and magnesium(II)
Keywords keywordsOXIDOREDUCTASE, OXIDATIVE BETA-DECARBOXYLATION; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.50 Å
Radius of gyration Rg (electron density) rg_electron22.50 Å
Forward intensity I(0) i034915900.00
Molecular weight molecular_weight45928.0 kDa
Excluded volume excluded_volume57730 ų
Envelope volume envelope_volume70203 ų
Hydration-shell volume shell_volume25760 ų
Envelope diameter envelope_diameter77.8 Å
Shell Rg shell_rg29.76 Å
Envelope Rg envelope_rg23.04 Å
Shape Rg shape_rg22.50 Å
Total Rg total_rg23.39 Å
Total atoms total_atoms3223
Residues n_residues415
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax76.2 Å
Rg (real space) rg_real23.42 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real3.4920e+07
I(0) uncertainty (real space) i0_real_error4.5540e+05
Rg (reciprocal space) rg_reciprocal23.44 Å
I(0) (reciprocal space) i0_reciprocal34920000.0000
Solution quality estimate total_estimate0.6918
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.1 Å
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.338
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5248000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 1.000; Smooth: 0.994
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4bnpa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamilyc.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family familyc.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

CATH v4.4 (1 domains)

Domain ID domain_id4bnpA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily10 — Isopropylmalate Dehydrogenase
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8. Citations (1)

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9. Files and Curves (10)