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Yorodumi- PDB-8ppi: Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ppi | |||||||||
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Title | Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate/ATP/Mn | |||||||||
Components | Inositol-trisphosphate 3-kinase A | |||||||||
Keywords | TRANSFERASE / Inositol polyphosphate / InsP / inositol kinase / IP3K / calcium / InsP3 / IP3 / IPK / IP3 3-K | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å | |||||||||
Authors | Marquez-Monino, M.A. / Gonzalez, B. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Nat Commun / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ppi.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ppi.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ppi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ppi_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 8ppi_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 8ppi_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 8ppi_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/8ppi ftp://data.pdbj.org/pub/pdb/validation_reports/pp/8ppi | HTTPS FTP |
-Related structure data
Related structure data | 8pp8C 8pp9C 8ppaC 8ppbC 8ppcC 8ppdC 8ppeC 8ppfC 8ppgC 8pphC 8ppjC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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.) Homo sapiens (human) / Gene: ITPKA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star References: UniProt: P23677, inositol-trisphosphate 3-kinase |
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-Non-polymers , 5 types, 485 molecules
#2: Chemical | Mass: 434.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17O15P3 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 % / Description: Cube / Trapezoidal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 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. ...Details: 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. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 6, 2021 / Details: KB mirror, elliptical beam shape |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873128 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→193.16 Å / Num. obs: 77850 / % possible obs: 91.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 25.115 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4142 / CC1/2: 0.62 / Rpim(I) all: 0.493 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.65→96.58 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.039 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 35.226 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→96.58 Å
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