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Yorodumi- PDB-6ohr: Structure of compound 5 bound human Phospholipase D1 catalytic domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ohr | ||||||
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Title | Structure of compound 5 bound human Phospholipase D1 catalytic domain | ||||||
Components | Phospholipase D1, chimeric constuct | ||||||
Keywords | hydrolase/hydrolase inhibitor / phosphodiesterase / HYDROLASE / HKD motif / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information : / Synthesis of PG / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / phospholipase D activity / phospholipid catabolic process / cholinergic synapse ...: / Synthesis of PG / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / phospholipase D activity / phospholipid catabolic process / cholinergic synapse / regulation of synaptic vesicle cycle / regulation of vesicle-mediated transport / small GTPase-mediated signal transduction / tertiary granule membrane / CDC42 GTPase cycle / endocytic vesicle / RHOG GTPase cycle / RHOA GTPase cycle / Role of phospholipids in phagocytosis / specific granule membrane / RAC1 GTPase cycle / phosphatidylinositol binding / positive regulation of translation / chemotaxis / late endosome membrane / Ras protein signal transduction / endosome / apical plasma membrane / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Metrick, C.M. / Chodaparambil, J.V. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: Human PLD structures enable drug design and characterization of isoenzyme selectivity. Authors: Metrick, C.M. / Peterson, E.A. / Santoro, J.C. / Enyedy, I.J. / Murugan, P. / Chen, T. / Michelsen, K. / Cullivan, M. / Spilker, K.A. / Kumar, P.R. / May-Dracka, T.L. / Chodaparambil, J.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ohr.cif.gz | 650 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ohr.ent.gz | 526.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ohr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/6ohr ftp://data.pdbj.org/pub/pdb/validation_reports/oh/6ohr | HTTPS FTP |
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-Related structure data
Related structure data | 6ohmSC 6ohoC 6ohpC 6ohqC 6ohsC 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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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 73987.852 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLD1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13393, phospholipase D #2: Chemical | ChemComp-MKG / |
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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: 2.22 Å3/Da / Density % sol: 44.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.1M Tris-HCl pH 8.8, 2.81M sodium acetate pH 7.6, 0.04-0.05M glycine pH 9.5, 0.3-0.5 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 66130 / % possible obs: 99.8 % / Redundancy: 31.1 % / CC1/2: 0.99 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 3.2→4 Å / Num. unique obs: 6614 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OHM Resolution: 3.2→48.362 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→48.362 Å
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Refine LS restraints |
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LS refinement shell |
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