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Yorodumi- PDB-5ywx: Crystal structure of hematopoietic prostaglandin D synthase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ywx | ||||||
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Title | Crystal structure of hematopoietic prostaglandin D synthase in complex with F092 | ||||||
Components | Hematopoietic prostaglandin D synthase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PROSTAGLANDIN / SYNTHASE / Inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior ...prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior / intracellular membrane-bounded organelle / calcium ion binding / magnesium ion binding / signal transduction / protein homodimerization activity / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å | ||||||
Authors | Kamo, M. / Furubayashi, N. / Inaka, K. / Aritake, K. / Omura, A. / Tanaka, A. | ||||||
Citation | Journal: Bioorg. Med. Chem. / Year: 2018 Title: Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies. Authors: Takaya, D. / Inaka, K. / Omura, A. / Takenuki, K. / Kawanishi, M. / Yabuki, Y. / Nakagawa, Y. / Tsuganezawa, K. / Ogawa, N. / Watanabe, C. / Honma, T. / Aritake, K. / Urade, Y. / Shirouzu, M. / Tanaka, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ywx.cif.gz | 193 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ywx.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 5ywx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/5ywx ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5ywx | HTTPS FTP |
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-Related structure data
Related structure data | 2cvdS S: Starting model for refinement |
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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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23239.637 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPGDS, GSTS, PGDS, PTGDS2 / Production host: Escherichia coli (E. coli) References: UniProt: O60760, prostaglandin-D synthase, glutathione transferase |
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-Non-polymers , 5 types, 596 molecules
#2: Chemical | ChemComp-GSH / #3: Chemical | ChemComp-93C / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 44.49 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 8.5 Details: 35% PEG6000, 5 mM DTT, 2 mM MgCl2, 2 mM Glutathione, 2% Dioxane, 50 mM Tris-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2014 | ||||||||||||||||||||||||
Radiation | Monochromator: Rotated-inclined double-crystal monochromator , Si (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.74→47.04 Å / Num. obs: 79469 / % possible obs: 97.1 % / Redundancy: 3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.072 / Rrim(I) all: 0.126 / Net I/σ(I): 5.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CVD Resolution: 1.74→47.04 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 2.98 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1449 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.141 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 104.34 Å2 / Biso mean: 21.977 Å2 / Biso min: 4.34 Å2
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Refinement step | Cycle: final / Resolution: 1.74→47.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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