3lcb

The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.

Method: X-RAY DIFFRACTION D_max: 172.2 Å Quality: REASONABLE

▼

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

Isocitrate dehydrogenase kinase/phosphatase

Escherichia coli

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–578	Not recorded	Isocitrate dehydrogenase [NADP] × 1 （P08200） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–578	Not recorded	Isocitrate dehydrogenase [NADP] × 1 （P08200） 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
3	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–578 Chain B； UniProt 1–578	Not recorded	Isocitrate dehydrogenase [NADP] × 6 （P08200） 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

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 3LCB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3LC6 The alternative conformation structure of isocitrate dehydrogenase kinase/phosphatase from E. Coli Deposited 2010-01-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–579（578 aa） Chain B 2–579（578 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；295 K；12% PEG 8000, 0.001M calcium chloride, 0.2M magnesium chloride, 0.1M MES 15% Glycerol, 0.002M DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.332
3LC6 The alternative conformation structure of isocitrate dehydrogenase kinase/phosphatase from E. Coli Deposited 2010-01-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–579（578 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；295 K；12% PEG 8000, 0.001M calcium chloride, 0.2M magnesium chloride, 0.1M MES 15% Glycerol, 0.002M DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.332
3LC6 The alternative conformation structure of isocitrate dehydrogenase kinase/phosphatase from E. Coli Deposited 2010-01-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–579（578 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；295 K；12% PEG 8000, 0.001M calcium chloride, 0.2M magnesium chloride, 0.1M MES 15% Glycerol, 0.002M DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.332

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ACEK_ECO5E
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–578； UniProt 1–578 Author chain B； PDBConstruct 1–578； UniProt 1–578

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–416	Not recorded	Isocitrate dehydrogenase kinase/phosphatase × 1 （B5Z0A8） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–416	Not recorded	Isocitrate dehydrogenase kinase/phosphatase × 1 （B5Z0A8） 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
3	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain C； UniProt 1–416 Chain D； UniProt 1–416	Not recorded	Isocitrate dehydrogenase kinase/phosphatase × 6 （B5Z0A8） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3LCB	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
4BNP 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate and magnesium(II) Deposited 2013-05-16	Different mutation/modification Different oligomeric state 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	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
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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IDH_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–416； UniProt 1–416 Author chain D； 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

P(r) Distance Distribution P(r) Distribution

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3lcb
Deposition date deposition_date	2010-01-10
Structure title title	The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.
Keywords keywords	KINASE PHOSPHATASE, GLYOXYLATE BYPASS, HYDROLASEPROTEIN PHOSPHATASE, TRICARBOXYLIC ACID CYCLE, Isocitrate, TRANSFERASE, HYDROLASE; TRANSFERASE, HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	49.54 Å
Radius of gyration Rg (electron density) rg_electron	49.97 Å
Forward intensity I(0) i0	709678000.00
Molecular weight molecular_weight	223560.0 kDa
Excluded volume excluded_volume	280620 Å³
Envelope volume envelope_volume	381700 Å³
Hydration-shell volume shell_volume	65249 Å³
Envelope diameter envelope_diameter	186.4 Å
Shell Rg shell_rg	51.26 Å
Envelope Rg envelope_rg	49.84 Å
Shape Rg shape_rg	49.96 Å
Total Rg total_rg	50.05 Å
Total atoms total_atoms	15750
Residues n_residues	1945
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

▼

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

Maximum dimension Dmax dmax	172.2 Å
Rg (real space) rg_real	50.10 Å
Rg uncertainty (real space) rg_real_error	1.83 Å
I(0) (real space) i0_real	7.0970e+08
I(0) uncertainty (real space) i0_real_error	1.2480e+07
Rg (reciprocal space) rg_reciprocal	49.54 Å
I(0) (reciprocal space) i0_reciprocal	709200000.0000
Solution quality estimate total_estimate	0.6047
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.0 Å
Skewness Skewness skewness	0.495
Kurtosis Kurtosis kurtosis	-0.455
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	106300000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 0.087; Positv: 1.000; Valcen: 0.793; Smooth: 0.652

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Isocitrate dehydrogenase kinase/phosphatase
Molecular weight formula_weight	67823.6 kDa
EC 编号 ec_number	2.7.11.5, 3.1.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	15771

MPRGLELLIAQTILQGFDAQYGRFLEVTSGAQQRFEQADWHAVQQAMKNRIHLYDHHVGLVVEQLRCITNGQSTDAEFLLRVKEHYTRLLPDYPRFEIAESFFNSVYCRLFDHRSLTPERLFIFSSQPERRFRTIPRPLAKDFHPDHGWESLLMRVISDLPLRLHWQNKSRDIHYIIRHLTETLGPENLSKSHLQVANELFYRNKAAWLVGKLITPSGTLPFLLPIHQTDDGELFIDTCLTTTAEASIVFGFARSYFMVYAPLPAALVEWLREILPGKTTAELYMAIGCQKHAKTESYREYLVYLQGCNEQFIEAPGIRGMVMLVFTLPGFDRVFKVIKDKFAPQKEMSAAHVRACYQLVKEHDRVGRMADTQEFENFVLEKRHISPALMELLLQEAAEKITDLGEQIVIRHLYIERRMVPLNIWLEQVEGQQLRDAIEEYGNAIRQLAAANIFPGDMLFKNFGVTRHGRVVFYDYDEICYMTEVNFRDIPPPRYPEDELASEPWYSVSPGDVFPEEFRHWLCADPRIGPLFEEMHADLFRADYWRALQNRIREGHVEDVYAYRRRQRFSVRYGEMLF

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83334
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Isocitrate dehydrogenase [NADP]
Molecular weight formula_weight	45809.6 kDa
EC 编号 ec_number	1.1.1.42
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3lcbc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

Domain ID domain_id	d3lcbd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

CATH v4.4 (2 domains)

Domain ID domain_id	3lcbC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

Domain ID domain_id	3lcbD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

▶

8. Citations (1)

▶

Unit-cell length a length_a	196.801 Å
Unit-cell length b length_b	196.801 Å
Unit-cell length c length_c	156.458 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1920
R_work r_work	0.1900
R_free r_free	0.2220

fit	/app/data/saxs_computation/lc/3lcb/3lcb.fit
pddf	/app/data/pr_computation/lc/3lcb/3lcb.pr.out
profile	/app/data/saxs_computation/lc/3lcb/3lcb.dat

The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.

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

Isocitrate dehydrogenase kinase/phosphatase

State in the Current Structure

Other States of the Same Protein in the Database

Isocitrate dehydrogenase [NADP]

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)