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Yorodumi- PDB-7qie: Crystal Structure of Phosphatidylinositol 5-Phosphate 4-Kinase (P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qie | ||||||
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Title | Crystal Structure of Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C) bound to an allosteric inhibitor | ||||||
Components | Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma | ||||||
Keywords | TRANSFERASE / ALLOSTERIC BINDING / LIPID KINASE / NON-ATP-COMPETITIVE INHIBITOR / phosphatidylinositol 5-phosphate | ||||||
Function / homology | Function and homology information 1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / intracellular organelle / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / intracellular organelle / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / autophagosome / negative regulation of insulin receptor signaling pathway / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phosphorylation / endoplasmic reticulum / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Howard, T.D. / Ogg, D.T. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Development of Selective Phosphatidylinositol 5-Phosphate 4-Kinase gamma Inhibitors with a Non-ATP-competitive, Allosteric Binding Mode. Authors: Boffey, H.K. / Rooney, T.P.C. / Willems, H.M.G. / Edwards, S. / Green, C. / Howard, T. / Ogg, D. / Romero, T. / Scott, D.E. / Winpenny, D. / Duce, J. / Skidmore, J. / Clarke, J.H. / Andrews, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qie.cif.gz | 511.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qie.ent.gz | 422 KB | Display | PDB format |
PDBx/mmJSON format | 7qie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/7qie ftp://data.pdbj.org/pub/pdb/validation_reports/qi/7qie | HTTPS FTP |
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-Related structure data
Related structure data | 7qpnC 2gk9S S: Starting model for refinement 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 42017.918 Da / Num. of mol.: 4 / Mutation: 300-341deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4K2C, PIP5K2C / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold References: UniProt: Q8TBX8, 1-phosphatidylinositol-5-phosphate 4-kinase #2: Chemical | ChemComp-DVF / #3: Water | ChemComp-HOH / | 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: 2.58 Å3/Da / Density % sol: 52.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 22% w/v Peg3350, 0.3 M Ammonium Tartrate, 100mM PCPT pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→146.17 Å / Num. obs: 36705 / % possible obs: 72.6 % / Redundancy: 3.7 % / CC1/2: 0.8387 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.39→2.46 Å / Num. unique obs: 83 / CC1/2: 0.359 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GK9 Resolution: 2.39→146.17 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.885 / SU B: 27.896 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 159.12 Å2 / Biso mean: 57.761 Å2 / Biso min: 14.98 Å2
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Refinement step | Cycle: final / Resolution: 2.39→146.17 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.395→2.457 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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