+Open data
-Basic information
Entry | Database: PDB / ID: 2vd1 | ||||||
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Title | Complex structure of prostaglandin D2 synthase at 2.25A. | ||||||
Components | GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE | ||||||
Keywords | ISOMERASE / PROSTAGLANDIN BIOSYNTHESIS / FATTY ACID BIOSYNTHESIS / PROSTAGLANDIN D2 SYNTHASE / PGDS / ASTHMA / CYTOPLASM / LIPID SYNTHESIS | ||||||
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 / Resolution: 2.25 Å | ||||||
Authors | Hohwy, M. / Spadola, L. / Lundquist, B. / von Wachenfeldt, K. / Persdotter, S. / Hawtin, P. / Dahmen, J. / Groth-Clausen, I. / Folmer, R.H.A. / Edman, K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Novel Prostaglandin D Synthase Inhibitors Generated by Fragment-Based Drug Design. Authors: Hohwy, M. / Spadola, L. / Lundquist, B. / Hawtin, P. / Dahmen, J. / Groth-Clausen, I. / Nilsson, E. / Persdotter, S. / Von Wachenfeldt, K. / Folmer, R.H.A. / Edman, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vd1.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vd1.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/2vd1 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/2vd1 | HTTPS FTP |
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-Related structure data
Related structure data | 2vcqC 2vcwC 2vcxC 2vczC 2vd0C 1pd2S C: citing same article (ref.) 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
#1: Protein | Mass: 23370.830 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: THE PROTEIN CONTAIN A GLUTATHIONE CO-FACTOR. / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60760, prostaglandin-D synthase #2: Chemical | ChemComp-GSH / #3: Chemical | ChemComp-D28 / | #4: Chemical | ChemComp-MG / | #5: 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 8.4 Details: PEG 6000 30%, TCEP 5MM, GSH 5MM, DIOXANE 1%, MGCL2 5MM, TRISHCL (PH8.4) 50 MM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9786 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→87 Å / Num. obs: 37285 / % possible obs: 98.5 % / Observed criterion σ(I): 1.7 / Redundancy: 3.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.7 / % possible all: 97.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PD2 Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.881 / SU B: 7.174 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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