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Yorodumi- PDB-6m8d: Crystal structure of the core catalytic domain of human inositol ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m8d | ||||||
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Title | Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with diosmetin | ||||||
Components | Inositol polyphosphate multikinase,Inositol polyphosphate multikinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE Inhibitor / kinase / inositol / inositol polyphosphate / TRANSFERASE / diosmetin / flavonoid / inhibitor / natural product / TRANSFERASE-TRANSFERASE Inhibitor complex | ||||||
Function / homology | Function and homology information Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity ...Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / inositol trisphosphate metabolic process / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate metabolic process / inositol phosphate biosynthetic process / phosphatidylinositol metabolic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / necroptotic process / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Wang, H. / Shears, S.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2019 Title: Inhibition of Inositol Polyphosphate Kinases by Quercetin and Related Flavonoids: A Structure-Activity Analysis. Authors: Gu, C. / Stashko, M.A. / Puhl-Rubio, A.C. / Chakraborty, M. / Chakraborty, A. / Frye, S.V. / Pearce, K.H. / Wang, X. / Shears, S.B. / Wang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m8d.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m8d.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 6m8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/6m8d ftp://data.pdbj.org/pub/pdb/validation_reports/m8/6m8d | HTTPS FTP |
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-Related structure data
Related structure data | 6m88C 6m89C 6m8aC 6m8bC 6m8cC 6m8eC 5w2gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29827.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IPMK, IMPK / Production host: Escherichia coli (E. coli) References: UniProt: Q8NFU5, inositol-polyphosphate multikinase |
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#2: Chemical | ChemComp-J8D / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 43.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG ...Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 10 mM diosmetin for 3 days. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 18315 / % possible obs: 99.5 % / Redundancy: 7.8 % / Biso Wilson estimate: 22.79 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.032 / Rrim(I) all: 0.096 / Χ2: 1.064 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 8 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 877 / CC1/2: 0.786 / Rpim(I) all: 0.317 / Rrim(I) all: 0.955 / Χ2: 0.84 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5w2g Resolution: 2→38 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.811 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R Free: 0.173 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.474 Å2
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Refinement step | Cycle: 1 / Resolution: 2→38 Å
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Refine LS restraints |
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