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Yorodumi- PDB-2bp2: THE STRUCTURE OF BOVINE PANCREATIC PROPHOSPHOLIPASE A2 AT 3.0 ANG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bp2 | ||||||
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Title | THE STRUCTURE OF BOVINE PANCREATIC PROPHOSPHOLIPASE A2 AT 3.0 ANGSTROMS RESOLUTION | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE ZYMOGEN | ||||||
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 / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process ...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 / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / phospholipase A2 / bile acid binding / arachidonic acid 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: 3 Å | ||||||
Authors | Dijkstra, B.W. / Vannes, G.J.H. / Kalk, K.H. / Brandenburg, N.P. / Hol, W.G.J. / Drenth, J. | ||||||
Citation | 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. #1: 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. #2: Journal: Nature / Year: 1981 Title: Active Site and Catalytic Mechanism of Phospholipase A2 Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H. #3: Journal: Thesis / Year: 1980 Title: Structure and Mechanism of Phospholipase A2 Authors: Dijkstra, B.W. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bp2.cif.gz | 31.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bp2.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bp2 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bp2 | 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 ABOVE. |
-Components
#1: Protein | Mass: 14539.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00593 |
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Compound details | THE ZYMOGEN PROPHOSPHOLIPASE A2 CONTAINS SEVEN EXTRA RESIDUES AT THE N-TERMINUS COMPARED WITH THE ...THE ZYMOGEN PROPHOSPHO |
Sequence details | SEQUENCE NUMBERING IS THE SAME AS FOR THE ACTIVE ENZYME, I. E. THE FIRST RESIDUE IS NUMBERED -7. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.9 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.6 / Method: unknown / Details: Dijkstra, B.W., (1978) J.Mol.Biol., 124, 53. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Rfactor Rwork: 0.219 / Highest resolution: 3 Å Details: RESIDUES 1 TO 3 INCLUSIVE AND 62 TO 73 INCLUSIVE ARE VIRTUALLY INVISIBLE IN ELECTRON DENSITY MAPS AND ARE PROBABLY DISORDERED. THE COORDINATES GIVEN BELOW FOR THESE RESIDUES CONTAIN, ...Details: RESIDUES 1 TO 3 INCLUSIVE AND 62 TO 73 INCLUSIVE ARE VIRTUALLY INVISIBLE IN ELECTRON DENSITY MAPS AND ARE PROBABLY DISORDERED. THE COORDINATES GIVEN BELOW FOR THESE RESIDUES CONTAIN, THEREFORE, VERY LARGE ERRORS. | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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Refinement | *PLUS Lowest resolution: 7.1 Å / Rfactor obs: 0.219 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |