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Yorodumi- PDB-3bp2: ROLE OF THE N-TERMINUS IN THE INTERACTION OF PANCREATIC PHOSPHOLI... -
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-Basic information
Entry | Database: PDB / ID: 3bp2 | |||||||||
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Title | ROLE OF THE N-TERMINUS IN THE INTERACTION OF PANCREATIC PHOSPHOLIPASE A2 WITH AGGREGATED SUBSTRATES. PROPERTIES AND CRYSTAL STRUCTURE OF TRANSAMINATED PHOSPHOLIPASE A2 | |||||||||
Components | PHOSPHOLIPASE A2 | |||||||||
Keywords | CARBOXYLIC ESTER HYDROLASE | |||||||||
Function / homology | Function and homology information Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / innate immune response in mucosa / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-positive bacterium / signaling receptor binding / calcium ion binding / cell surface / extracellular space Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | |||||||||
Authors | Dijkstra, B.W. / Drenth, J. | |||||||||
Citation | Journal: Biochemistry / Year: 1984 Title: Role of the N-terminus in the interaction of pancreatic phospholipase A2 with aggregated substrates. Properties and crystal structure of transaminated phospholipase A2 Authors: Dijkstra, B.W. / Kalk, K.H. / Drenth, J. / de Haas, G.H. / Egmond, M.R. / Slotboom, A.J. #1: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of Porcine Pancreatic Phospholipase A2 at 2.6 Angstroms Resolution and Comparison with Bovine Phospholipase A2 Authors: Dijkstra, B.W. / Renetseder, R. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. #2: 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. #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: 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. #5: 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 | 3bp2.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bp2.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bp2_validation.pdf.gz | 367.1 KB | Display | wwPDB validaton report |
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Full document | 3bp2_full_validation.pdf.gz | 374.5 KB | Display | |
Data in XML | 3bp2_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 3bp2_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/3bp2 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bp2 | HTTPS FTP |
-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 5. |
-Components
#1: Protein | Mass: 13809.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00593, phospholipase A2 |
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#2: Chemical | ChemComp-CA / |
#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: 2.08 Å3/Da / Density % sol: 40.85 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.6 / Method: unknownDetails: referred to 'Dijkstra, B.W.', (1978) J.Mol.Biol., 124, 53-60 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 9999 Å / Num. all: 7160 / Num. obs: 5435 / % possible obs: 76 % / Rmerge F obs: 0.062 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Rfactor Rwork: 0.174 / Highest resolution: 2.1 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
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Refinement | *PLUS Lowest resolution: 7.1 Å / Rfactor Rwork: 0.173 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |