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Yorodumi- PDB-1p2p: STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 AT 2.6 ANGSTROMS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p2p | ||||||
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Title | STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 AT 2.6 ANGSTROMS RESOLUTION AND COMPARISON WITH BOVINE PHOSPHOLIPASE A2 | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | CARBOXYLIC ESTER HYDROLASE | ||||||
Function / homology | Function and homology information Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / phospholipid binding / positive regulation of MAP kinase activity / cellular response to insulin stimulus / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / positive regulation of immune response / positive regulation of NF-kappaB transcription factor activity / intracellular signal transduction / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Dijkstra, B.W. / Renetseder, R. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1983 Title: Structure of porcine pancreatic phospholipase A2 at 2.6 A resolution and comparison with bovine phospholipase A2. Authors: Dijkstra, B.W. / Renetseder, R. / Kalk, K.H. / Hol, W.G. / Drenth, J. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1982 Title: The Structure of Bovine Pancreatic Prophospholipase A2 at 3.0 Angstroms Resolution Authors: Dijkstra, B.W. / Vannes, G.J.H. / Kalk, K.H. / Brandenburg, N.P. / Hol, W.G.J. / Drenth, J. #2: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of Bovine Pancreatic Phospholipase A2 at 1.7 Angstroms Resolution Authors: Dijkstra, B.W. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. #3: Journal: Nature / Year: 1981 Title: Active Site and Catalytic Mechanism of Phospholipase A2 Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H. #4: Journal: J.Mol.Biol. / Year: 1978 Title: Three-Dimensional Structure and Disulfide Bond Connections in Bovine Pancreatic Phospholipase A2 Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H. / Vandermaelen, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p2p.cif.gz | 32.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p2p.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 1p2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/1p2p ftp://data.pdbj.org/pub/pdb/validation_reports/p2/1p2p | 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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Unit cell |
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Atom site foot note | 1: SEE REMARK 8. / 2: SEE REMARK 4. | ||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14009.714 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00592, phospholipase A2 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Compound details | THE TYPE CLASSIFICATIONS GIVEN IN THE REMARK FIELD OF THE TURN RECORDS BELOW FOLLOWS THE ...THE TYPE CLASSIFICA | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.79 % | ||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: unknown | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. all: 6144 / Num. obs: 4603 / % possible obs: 74.9 % / Rmerge(I) obs: 0.058 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.241 / Highest resolution: 2.6 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.6 Å
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Refinement | *PLUS Lowest resolution: 7 Å / Num. reflection obs: 4295 / Rfactor obs: 0.241 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.5 Å2 | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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