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- PDB-5jan: Exploitation of a Novel Binding Pocket in Human Lipoprotein-Assoc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jan | ||||||
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Title | Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered Through X-Ray Fragment Screening | ||||||
![]() | Platelet-activating factor acetylhydrolase | ||||||
![]() | HYDROLASE / phospholipase / lipid metabolism | ||||||
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 | ![]() | ||||||
![]() | Day, P.J. | ||||||
![]() | ![]() Title: Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening. Authors: Woolford, A.J. / Pero, J.E. / Aravapalli, S. / Berdini, V. / Coyle, J.E. / Day, P.J. / Dodson, A.M. / Grondin, P. / Holding, F.P. / Lee, L.Y. / Li, P. / Manas, E.S. / Marino, J. / Martin, A. ...Authors: Woolford, A.J. / Pero, J.E. / Aravapalli, S. / Berdini, V. / Coyle, J.E. / Day, P.J. / Dodson, A.M. / Grondin, P. / Holding, F.P. / Lee, L.Y. / Li, P. / Manas, E.S. / Marino, J. / Martin, A.C. / McCleland, B.W. / McMenamin, R.L. / Murray, C.W. / Neipp, C.E. / Page, L.W. / Patel, V.K. / Potvain, F. / Rich, S. / Rivero, R.A. / Smith, K. / Somers, D.O. / Trottet, L. / Velagaleti, R. / Williams, G. / Xie, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.4 KB | Display | ![]() |
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PDB format | ![]() | 130.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5jadC ![]() 5jahC ![]() 5jalC ![]() 5jaoC ![]() 5japC ![]() 5jarC ![]() 5jasC ![]() 5jatC ![]() 5jauC 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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Unit cell |
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Components
#1: Protein | Mass: 44203.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13093, 1-alkyl-2-acetylglycerophosphocholine esterase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-6HP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 1.0M NaCl, 0.1M HEPES/NaOHpH=7.4, 28.8%w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→46.33 Å / Num. obs: 21778 / % possible obs: 99.2 % / Redundancy: 3.6 % / Net I/σ(I): 7.5 |
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Processing
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Refinement | Resolution: 2.12→46.33 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 16.474 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.219 / 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: 34.96 Å2
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Refinement step | Cycle: 1 / Resolution: 2.12→46.33 Å
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Refine LS restraints |
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