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Yorodumi- PDB-8a5x: Crystal structure of phosphatidyl inositol 4-kinase II beta in co... -
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-Basic information
Entry | Database: PDB / ID: 8a5x | ||||||
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Title | Crystal structure of phosphatidyl inositol 4-kinase II beta in complex with MM1373 | ||||||
Components | Phosphatidylinositol 4-kinase type 2-beta,Endolysin | ||||||
Keywords | TRANSFERASE / lipid / kinase / PI4K2B / inhibitor | ||||||
Function / homology | Function and homology information Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / endosome organization / phosphatidylinositol biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / endosome organization / phosphatidylinositol biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / viral release from host cell by cytolysis / peptidoglycan catabolic process / phosphorylation / trans-Golgi network / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / early endosome membrane / host cell cytoplasm / endosome / defense response to bacterium / Golgi membrane / endoplasmic reticulum membrane / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Klima, M. / Boura, E. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2022 Title: Structure-based design and modular synthesis of novel PI4K class II inhibitors bearing a 4-aminoquinazoline scaffold. Authors: Misehe, M. / Klima, M. / Matousova, M. / Chalupska, D. / Dejmek, M. / Sala, M. / Mertlikova-Kaiserova, H. / Boura, E. / Nencka, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a5x.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a5x.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 8a5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/8a5x ftp://data.pdbj.org/pub/pdb/validation_reports/a5/8a5x | HTTPS FTP |
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-Related structure data
Related structure data | 4wtvS S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 59367.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PI4K2B / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8TCG2, UniProt: P00720, 1-phosphatidylinositol 4-kinase, lysozyme |
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#2: Chemical | ChemComp-L6A / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 10% w/v PEG 8.000, 20% v/v ethylene glycol, 3% v/v DMSO, 100 mM bicine/Trizma base pH 8.5, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4- ...Details: 10% w/v PEG 8.000, 20% v/v ethylene glycol, 3% v/v DMSO, 100 mM bicine/Trizma base pH 8.5, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→31.63 Å / Num. obs: 20410 / % possible obs: 92.17 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.31 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.09953 / Rpim(I) all: 0.05996 / Rrim(I) all: 0.1164 / Net I/σ(I): 13.38 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6079 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 1863 / CC1/2: 0.764 / CC star: 0.931 / Rpim(I) all: 0.3578 / Rrim(I) all: 0.7059 / % possible all: 84.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WTV Resolution: 2.4→31.63 Å / SU ML: 0.2735 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9157 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→31.63 Å
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Refine LS restraints |
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LS refinement shell |
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