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 | 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 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 188–461 | 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 |
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 8PP9 | 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 |
| 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 |
| 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 | 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 × 1 661 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 | 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 × 1 661 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 | 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 |
