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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P23677 New Search
17PDB entries
33Biological assembly
38chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method 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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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
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 Deposited 2023-07-07 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 188–461（274 aa）
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
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 Deposited 2023-07-07 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 188–461（274 aa）
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
9QGK F-actin decorated by ITPKA Deposited 2025-03-13 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric（13） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.