8ppj

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,6,1'-tetrakisphosphate/ADP/Mn after reaction

Method: X-RAY DIFFRACTION D_max: 85.1 Å Quality: GOOD

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

Inositol-trisphosphate 3-kinase A

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 188–461	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 661 beta-D-glucopyranosylmethanol 3,4,6,1'-tetrakisphosphate × 1 SO4 SULFATE ION × 4 MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.80 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking overnight with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.	Resolution 1.75 Å R-free 0.234
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 188–461	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 661 beta-D-glucopyranosylmethanol 3,4,6,1'-tetrakisphosphate × 1 SO4 SULFATE ION × 4 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.80 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking overnight with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.	Resolution 1.75 Å R-free 0.234

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 8PPJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W2C Human Inositol (1,4,5) trisphosphate 3-kinase complexed with Mn2+/AMPPNP/Ins(1,4,5)P3 Deposited 2004-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 197–461（265 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 197-461	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.835 M NA CITRATE, 0.1 M NACL, 0.1 M TRIS PH=8, pH 8.00	Resolution 1.95 Å R-free 0.243
1W2C Human Inositol (1,4,5) trisphosphate 3-kinase complexed with Mn2+/AMPPNP/Ins(1,4,5)P3 Deposited 2004-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 197–461（265 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 197-461	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.835 M NA CITRATE, 0.1 M NACL, 0.1 M TRIS PH=8, pH 8.00	Resolution 1.95 Å R-free 0.243
1W2D Human Inositol (1,4,5)-trisphosphate 3-kinase complexed with Mn2+/ADP/Ins(1,3,4,5)P4 Deposited 2004-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 197–461（265 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 197-461	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.82 M NA CITRATE, 0.1 M NACL, 0.1 M TRIS PH 8.	Resolution 1.94 Å R-free 0.267
1W2D Human Inositol (1,4,5)-trisphosphate 3-kinase complexed with Mn2+/ADP/Ins(1,3,4,5)P4 Deposited 2004-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 197–461（265 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 197-461	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.82 M NA CITRATE, 0.1 M NACL, 0.1 M TRIS PH 8.	Resolution 1.94 Å R-free 0.267
1W2F Human Inositol (1,4,5)-trisphosphate 3-kinase substituted with selenomethionine Deposited 2004-07-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 187–461（275 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 186-461	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.9 M NA CITRATE, 0.1 M NACL, 0.1 M TRIS PH 8.	Resolution 1.80 Å R-free 0.241
1W2F Human Inositol (1,4,5)-trisphosphate 3-kinase substituted with selenomethionine Deposited 2004-07-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 187–461（275 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 186-461	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.9 M NA CITRATE, 0.1 M NACL, 0.1 M TRIS PH 8.	Resolution 1.80 Å R-free 0.241
4UPU Crystal structure of IP3 3-K calmodulin binding region in complex with Calmodulin Deposited 2014-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain B 158–183（26 aa） Fragment：CALMODULIN BINDING REGION, RESIDUES 158-183	Not recorded	CA CALCIUM ION × 120 GOL GLYCEROL × 24	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；29% W/V POLYETHYLENE GLYCOL 4000, 0.2 M (NH4)2SO4, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.0 AND 10 MM SPERMIDINE	Resolution 2.34 Å R-free 0.210
8PP8 Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with L-scyllo-inositol 1,2,4-trisphosphate/AMP-PNP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 3IA L-scyllo-inositol 1,2,4-trisphosphate × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MnCl2.	Resolution 1.59 Å R-free 0.212
8PP8 Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with L-scyllo-inositol 1,2,4-trisphosphate/AMP-PNP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 3IA L-scyllo-inositol 1,2,4-trisphosphate × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MnCl2.	Resolution 1.59 Å R-free 0.212
8PP9 Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with scyllo-inositol 1,2,3,5-tetrakisphosphate/ADP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	4IM scyllo-inositol 1,2,3,5-tetrakisphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ADP and 3 mM MnCl2.	Resolution 1.73 Å R-free 0.210
8PP9 Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with scyllo-inositol 1,2,3,5-tetrakisphosphate/ADP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	4IM scyllo-inositol 1,2,3,5-tetrakisphosphate × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ADP and 3 mM MnCl2.	Resolution 1.73 Å R-free 0.210
8PPA Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-myo-inositol 1,4,6-trisphosphate/AMP-PNP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 06G D-myo-inositol 1,4,6-trisphosphate × 1 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MnCl2.	Resolution 1.73 Å R-free 0.218
8PPA Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-myo-inositol 1,4,6-trisphosphate/AMP-PNP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 06G D-myo-inositol 1,4,6-trisphosphate × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MnCl2.	Resolution 1.73 Å R-free 0.218
8PPA Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-myo-inositol 1,4,6-trisphosphate/AMP-PNP/Mn Deposited 2023-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 188–461（274 aa） Chain B 188–461（274 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 06G D-myo-inositol 1,4,6-trisphosphate × 2 SO4 SULFATE ION × 6 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MnCl2.	Resolution 1.73 Å R-free 0.218
8PPB Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-3-deoxy-myo-inositol 1,4,6-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	3I2 D-3-deoxy-myo-inositol 1,4,6-trisphosphate × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.84 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.80 Å R-free 0.216
8PPB Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-3-deoxy-myo-inositol 1,4,6-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	3I2 D-3-deoxy-myo-inositol 1,4,6-trisphosphate × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.84 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.80 Å R-free 0.216
8PPC Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with L-chiro-inositol 2,3,5-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	2KM L-chiro-inositol 2,3,5-trisphosphate × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.80 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 9 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.92 Å R-free 0.219
8PPC Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with L-chiro-inositol 2,3,5-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	2KM L-chiro-inositol 2,3,5-trisphosphate × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.80 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 9 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.92 Å R-free 0.219
8PPD Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	SO4 SULFATE ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 75I DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.83 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 10 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.77 Å R-free 0.230
8PPD Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	SO4 SULFATE ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 75I DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.83 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 10 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.77 Å R-free 0.230
8PPE Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-phosphoryloxymethyl-scyllo-inositol 1,2,4-trisphosphate/ADP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 7I8 DL-6-deoxy-6-phosphoryloxymethyl-scyllo-inositol 1,2,4-trisphosphate × 1 GOL GLYCEROL × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking overnight with 0.83 M sodium citrate, 0.1 M Tris pH 8.5, 0.1 M NaCl, 30 mM ligand, 3 mM ADP and 3 mM MnCl2. Cryoprotectant: Glycerol 30%.	Resolution 1.59 Å R-free 0.240
8PPE Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-phosphoryloxymethyl-scyllo-inositol 1,2,4-trisphosphate/ADP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 7I8 DL-6-deoxy-6-phosphoryloxymethyl-scyllo-inositol 1,2,4-trisphosphate × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking overnight with 0.83 M sodium citrate, 0.1 M Tris pH 8.5, 0.1 M NaCl, 30 mM ligand, 3 mM ADP and 3 mM MnCl2. Cryoprotectant: Glycerol 30%.	Resolution 1.59 Å R-free 0.240
8PPF Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4-trisphosphate/AMP-PNP/Mg Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 6II beta-D-glucopyranosyl 1,3,4-trisphosphate × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MgCl2.	Resolution 1.85 Å R-free 0.228
8PPF Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4-trisphosphate/AMP-PNP/Mg Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 6II beta-D-glucopyranosyl 1,3,4-trisphosphate × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MgCl2.	Resolution 1.85 Å R-free 0.228
8PPG Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate/ADP/Mn after reaction Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	SO4 SULFATE ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 46I beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking overnight with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosyl 1,3,4-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.	Resolution 1.75 Å R-free 0.243
8PPG Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate/ADP/Mn after reaction Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	SO4 SULFATE ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 46I beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking overnight with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosyl 1,3,4-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.	Resolution 1.75 Å R-free 0.243
8PPH Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with alpha-D-glucopyranosyl 1,3,4-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 5AI alpha-D-glucopyranosyl 1,3,4-trisphosphate × 1 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.84 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.70 Å R-free 0.231
8PPH Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with alpha-D-glucopyranosyl 1,3,4-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.84 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.70 Å R-free 0.231
8PPI Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 188–461（274 aa）	Not recorded	69I beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.65 Å R-free 0.214
8PPI Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate/ATP/Mn Deposited 2023-07-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 188–461（274 aa）	Not recorded	69I beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 4 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.	Resolution 1.65 Å R-free 0.214
9QGK F-actin decorated by ITPKA Deposited 2025-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric	Chain A 1–461（461 aa） Chain B 1–461（461 aa） Chain C 1–461（461 aa） Chain D 1–461（461 aa） Chain E 1–461（461 aa）	Not recorded	MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.97 Å

16 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IP3KA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–279； UniProt 188–461 Author chain B； PDBConstruct 6–279； UniProt 188–461

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	8ppj
Deposition date deposition_date	2023-07-07
Structure title title	Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,6,1'-tetrakisphosphate/ADP/Mn after reaction
Keywords keywords	Inositol polyphosphate, InsP, inositol kinase, IP3K, calcium, InsP3, IP3, IPK, IP3 3-K, 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	26.26 Å
Radius of gyration Rg (electron density) rg_electron	25.38 Å
Forward intensity I(0) i0	77253500.00
Molecular weight molecular_weight	63789.0 kDa
Excluded volume excluded_volume	77748 Å³
Envelope volume envelope_volume	95904 Å³
Hydration-shell volume shell_volume	31190 Å³
Envelope diameter envelope_diameter	88.7 Å
Shell Rg shell_rg	32.99 Å
Envelope Rg envelope_rg	25.18 Å
Shape Rg shape_rg	25.44 Å
Total Rg total_rg	25.98 Å
Total atoms total_atoms	4435
Residues n_residues	532
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	85.1 Å
Rg (real space) rg_real	26.18 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	7.7250e+07
I(0) uncertainty (real space) i0_real_error	1.1070e+06
Rg (reciprocal space) rg_reciprocal	26.21 Å
I(0) (reciprocal space) i0_reciprocal	77250000.0000
Solution quality estimate total_estimate	0.8943
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	83.7 Å
Skewness Skewness skewness	0.266
Kurtosis Kurtosis kurtosis	-0.349
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11080000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.981

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Inositol-trisphosphate 3-kinase A
Molecular weight formula_weight	31877.3 kDa
EC 编号 ec_number	2.7.1.127
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	4896

GSHMSWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	;beta-D-glucopyranosylmethanol 3,4,6,1'-tetrakisphosphate ;
Molecular weight formula_weight	514.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	402

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8. Citations (1)

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Unit-cell length a length_a	72.530 Å
Unit-cell length b length_b	97.063 Å
Unit-cell length c length_c	191.127 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	95.560 Å
R factor r_factor	0.1989
R_work r_work	0.1971
R_free r_free	0.2342

fit	/app/data/saxs_computation/pp/8ppj/8ppj.fit
pddf	/app/data/pr_computation/pp/8ppj/8ppj.pr.out
profile	/app/data/saxs_computation/pp/8ppj/8ppj.dat