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Yorodumi- PDB-1kvo: HUMAN PHOSPHOLIPASE A2 COMPLEXED WITH A HIGHLY POTENT SUBSTRATE A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kvo | ||||||
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Title | HUMAN PHOSPHOLIPASE A2 COMPLEXED WITH A HIGHLY POTENT SUBSTRATE ANOLOGUE | ||||||
Components | HUMAN PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / LIPID DEGRADATION / MEMBRANE / CALCIUM | ||||||
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 / phosphatidylcholine metabolic process / positive regulation of macrophage derived foam cell differentiation / phospholipase A2 activity / low-density lipoprotein particle remodeling / calcium-dependent phospholipase A2 activity / phospholipase A2 / Antimicrobial peptides / arachidonate 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 Å | ||||||
Authors | Cha, S.-S. / Abdel-Meguid, S.S. / Oh, B.-H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1996 Title: High-resolution X-ray crystallography reveals precise binding interactions between human nonpancreatic secreted phospholipase A2 and a highly potent inhibitor (FPL67047XX). Authors: Cha, S.S. / Lee, D. / Adams, J. / Kurdyla, J.T. / Jones, C.S. / Marshall, L.A. / Bolognese, B. / Abdel-Meguid, S.S. / Oh, B.H. #1: Journal: To be Published Title: Structures of Free and Inhibited Human Secretory Phospholipase A2 from Inflammatory Exudate Authors: Scott, D.L. / White, S.P. / Browning, J.L. / Rosa, J.J. / Gelb, M.H. / Sigler, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kvo.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kvo.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kvo ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kvo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13945.012 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14555, phospholipase A2 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-OAP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 7 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MACSCIENCE / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 81302 / % possible obs: 95 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07 |
-Processing
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Refinement | Resolution: 2→8 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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