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- PDB-8ppj: Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ppj | |||||||||
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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 | |||||||||
![]() | Inositol-trisphosphate 3-kinase A | |||||||||
![]() | TRANSFERASE / Inositol polyphosphate / InsP / inositol kinase / IP3K / calcium / InsP3 / IP3 / IPK / IP3 3-K | |||||||||
Function / homology | ![]() inositol-trisphosphate 3-kinase / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / modification of postsynaptic actin cytoskeleton / inositol phosphate biosynthetic process / postsynaptic actin cytoskeleton / inositol metabolic process / positive regulation of dendritic spine morphogenesis / dendritic spine maintenance / calcium/calmodulin-dependent protein kinase activity ...inositol-trisphosphate 3-kinase / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / modification of postsynaptic actin cytoskeleton / inositol phosphate biosynthetic process / postsynaptic actin cytoskeleton / inositol metabolic process / positive regulation of dendritic spine morphogenesis / dendritic spine maintenance / calcium/calmodulin-dependent protein kinase activity / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol phosphate biosynthetic process / cellular response to calcium ion / regulation of synaptic plasticity / small GTPase binding / response to calcium ion / actin cytoskeleton organization / dendritic spine / cytoskeleton / calmodulin binding / phosphorylation / glutamatergic synapse / signal transduction / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Marquez-Monino, M.A. / Gonzalez, B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity. Authors: Marquez-Monino, M.A. / Ortega-Garcia, R. / Whitfield, H. / Riley, A.M. / Infantes, L. / Garrett, S.W. / Shipton, M.L. / Brearley, C.A. / Potter, B.V.L. / Gonzalez, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.1 KB | Display | ![]() |
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PDB format | ![]() | 105.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pp8C ![]() 8pp9C ![]() 8ppaC ![]() 8ppbC ![]() 8ppcC ![]() 8ppdC ![]() 8ppeC ![]() 8ppfC ![]() 8ppgC ![]() 8pphC ![]() 8ppiC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31877.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Catalytic domain / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P23677, inositol-trisphosphate 3-kinase |
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-Non-polymers , 5 types, 418 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | Mass: 514.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H18O18P4 / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % / Description: Cube / Trapezoidal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 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. ...Details: 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. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jul 23, 2022 / Details: Toroidal mirror, elliptical beam shape |
Radiation | Monochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→191.13 Å / Num. obs: 68270 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 29.4 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3749 / CC1/2: 0.661 / Rpim(I) all: 0.467 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.128 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→95.56 Å
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Refine LS restraints |
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