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- PDB-5jad: Compound binding to Human Lipoprotein-Associated Phospholipase A2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jad | ||||||
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Title | Compound binding to Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2)discovered through 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. / Woolford, A.J.-A. | ||||||
![]() | ![]() 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 | ![]() | 169.3 KB | Display | ![]() |
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PDB format | ![]() | 130.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.7 KB | Display | ![]() |
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Full document | ![]() | 451.8 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jahC ![]() 5jalC ![]() 5janC ![]() 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 147 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/FB2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/FB2.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-FB2 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 1.2M NaCl, 0.1M HEPES/NaOHpH=7.4, 28.8%w/v PEG 3350 PH range: 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 15, 2010 / Details: VariMax VHF Arc)Sec optic |
Radiation | Monochromator: VariMax VHF Arc)Sec optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→64 Å / Num. obs: 103331 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 28.81 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.05→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.3 / % possible all: 88.7 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Buster refinement was interspersed with rounds of rebuilding with COOT
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Displacement parameters | Biso mean: 33.676 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.05→32.31 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.05 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 30.0021 Å / Origin y: 14.7021 Å / Origin z: 0.8666 Å
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Refinement TLS group | Selection details: { A|55 - A|425 } |