+Open data
-Basic information
Entry | Database: PDB / ID: 6g5j | ||||||
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Title | Secreted phospholipase A2 type X in complex with ligand | ||||||
Components | Group 10 secretory phospholipase A2 | ||||||
Keywords | HYDROLASE / SECRETORY PHOSPHOLIPASE A2 TYPE X sPLA2X sPLA2-X phospholipase enzyme inhibitor complex | ||||||
Function / homology | Function and homology information phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / intestinal stem cell homeostasis / phospholipase activity ...phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / intestinal stem cell homeostasis / phospholipase activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Synthesis of PA / negative regulation of cholesterol efflux / arachidonic acid metabolic process / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity / phosphatidylcholine catabolic process / positive regulation of prostaglandin secretion / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / phosphatidylcholine metabolic process / macrophage activation / positive regulation of arachidonic acid secretion / low-density lipoprotein particle remodeling / fertilization / phospholipase A2 / phospholipase A2 activity / prostaglandin biosynthetic process / regulation of macrophage activation / arachidonic acid secretion / hair follicle morphogenesis / erythrocyte maturation / negative regulation of cytokine production involved in inflammatory response / phospholipid metabolic process / positive regulation of protein metabolic process / cellular response to leukemia inhibitory factor / acrosomal vesicle / cholesterol homeostasis / axon guidance / phospholipid binding / negative regulation of DNA-binding transcription factor activity / negative regulation of inflammatory response / defense response to virus / lysosome / calcium ion binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.85 Å | ||||||
Authors | Sandmark, J. / Oster, L. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2018 Title: Design of Selective sPLA2-X Inhibitor (-)-2-{2-[Carbamoyl-6-(trifluoromethoxy)-1H-indol-1-yl]pyridine-2-yl}propanoic Acid. Authors: Giordanetto, F. / Knerr, L. / Nordberg, P. / Pettersen, D. / Selmi, N. / Beisel, H.G. / de la Motte, H. / Mansson, A. / Dahlstrom, M. / Broddefalk, J. / Saarinen, G. / Klingegard, F. / Hurt- ...Authors: Giordanetto, F. / Knerr, L. / Nordberg, P. / Pettersen, D. / Selmi, N. / Beisel, H.G. / de la Motte, H. / Mansson, A. / Dahlstrom, M. / Broddefalk, J. / Saarinen, G. / Klingegard, F. / Hurt-Camejo, E. / Rosengren, B. / Wikstrom, J. / Wagberg, M. / Brengdahl, J. / Rohman, M. / Sandmark, J. / Akerud, T. / Roth, R.G. / Jansen, F. / Ahlqvist, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g5j.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g5j.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 6g5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g5j ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g5j | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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, 2 molecules AB
#1: Protein | Mass: 18171.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15496, phospholipase A2 |
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-Non-polymers , 5 types, 143 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-DMS / | #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 grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 37-45% PEG400 0.1M bis-Tris pH 5.6-5.9 / PH range: 5.6-5.9 / Temp details: RT |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.54 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.15 Å / Num. all: 71101 / Num. obs: 21588 / % possible obs: 91 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Resolution: 1.85→42.76 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.975 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.145 / 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: 23.567 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→42.76 Å
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