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- PDB-3f9c: Crystal structure of human plasma platelet activating factor acet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f9c | ||||||
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Title | Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by diisopropylfluorophosphate | ||||||
![]() | Platelet-activating factor acetylhydrolase | ||||||
![]() | HYDROLASE / PLASMA PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE / SECRETED PROTEIN / ALPHA/BETA-HYDROLASE-FOLD / LDL-BOUND / LIPOPROTEIN ASSOCIATED PHOSPHOLIPASE A2 / LP-PLA2 / GROUP VIIA PLA2 / GLYCOPROTEIN / LIPID DEGRADATION / POLYMORPHISM / DIISOPROPYLFLUOROPHOSPHATE / DFP / Disease mutation / Secreted | ||||||
Function / homology | ![]() plasma lipoprotein particle oxidation / platelet activating factor catabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid oxidation / phosphatidylcholine catabolic process / low-density lipoprotein particle / high-density lipoprotein particle ...plasma lipoprotein particle oxidation / platelet activating factor catabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid oxidation / phosphatidylcholine catabolic process / low-density lipoprotein particle / high-density lipoprotein particle / low-density lipoprotein particle remodeling / positive regulation of monocyte chemotaxis / peptide hormone processing / hydrolase activity, acting on ester bonds / Synthesis, secretion, and deacylation of Ghrelin / phospholipid binding / positive regulation of inflammatory response / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Samanta, U. / Bahnson, B.J. | ||||||
![]() | ![]() Title: Crystal structures of human group-VIIA phospholipase A2 inhibited by organophosphorus nerve agents exhibit non-aged complexes. Authors: Samanta, U. / Kirby, S.D. / Srinivasan, P. / Cerasoli, D.M. / Bahnson, B.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.7 KB | Display | ![]() |
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PDB format | ![]() | 127.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.7 KB | Display | ![]() |
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Full document | ![]() | 456.5 KB | Display | |
Data in XML | ![]() | 29.8 KB | Display | |
Data in CIF | ![]() | 42 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f96C ![]() 3f97C ![]() 3f98C ![]() 3d59S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 43494.367 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 47-429 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13093, 1-alkyl-2-acetylglycerophosphocholine esterase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: PH 6.6. NATIVE PROTEIN CRYSTAL SOAKED IN MOTHER LIQUOR CONTAINING DFP, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 15, 2008 / Details: OSMIC BLUE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 36675 / Num. obs: 36675 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.71 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.23 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NATIVE STRUCTURE, PDB ENTRY 3D59 Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.754 / SU ML: 0.19 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.358 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.908 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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