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Yorodumi- PDB-1dcy: CRYSTAL STRUCTURE OF HUMAN S-PLA2 IN COMPLEX WITH INDOLE 3 ACTIVE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dcy | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN S-PLA2 IN COMPLEX WITH INDOLE 3 ACTIVE SITE INHIBITOR | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / S-PLA2 / STRUCTURE-BASED DRUG DESIGN / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA ...regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / calcium-dependent phospholipase A2 activity / positive regulation of macrophage derived foam cell differentiation / phosphatidylcholine metabolic process / low-density lipoprotein particle remodeling / phospholipase A2 / phospholipase A2 activity / Antimicrobial peptides / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / secretory granule / phospholipid binding / positive regulation of inflammatory response / killing of cells of another organism / mitochondrial outer membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Chirgadze, N.Y. / Schevitz, R.W. / Wery, J.-P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1995 Title: Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2. Authors: Schevitz, R.W. / Bach, N.J. / Carlson, D.G. / Chirgadze, N.Y. / Clawson, D.K. / D Dillard, R. / Draheim, S.D. / Hartley, L.W. / Jones, N.D. / Mihelich, E.D. / L Olkowski, J. / Snyder, D.W. / ...Authors: Schevitz, R.W. / Bach, N.J. / Carlson, D.G. / Chirgadze, N.Y. / Clawson, D.K. / D Dillard, R. / Draheim, S.D. / Hartley, L.W. / Jones, N.D. / Mihelich, E.D. / L Olkowski, J. / Snyder, D.W. / Dand, S.C. / Wery, J.-P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dcy.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dcy.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/1dcy ftp://data.pdbj.org/pub/pdb/validation_reports/dc/1dcy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13945.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P14555, phospholipase A2 | ||||
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#2: Chemical | #3: Chemical | ChemComp-I3N / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion / pH: 7 Details: 10 MG/ML OF PROTEIN, 50 MM BUFFER (MES OF MOPS), 1% PYRIDINE, AN INHIBITOR CONCENTRATION OF 1.5 MOLAR EQUIVALENT, pH 7.0, VAPOR DIFFUSION, temperature 297K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 7.5 / PH range high: 6.6 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 14, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 4448 / % possible obs: 98.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.4 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % possible obs: 78 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.092 / Biso Wilson estimate: 25.5 Å2 |
-Processing
Software |
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Refinement | Resolution: 2.7→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 98 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Rfactor obs: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.336 / % reflection Rfree: 3.9 % / Rfactor Rwork: 0.297 |