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Yorodumi- PDB-1ppg: The refined 2.3 angstroms crystal structure of human leukocyte el... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ppg | ||||||||||||
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Title | The refined 2.3 angstroms crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor | ||||||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||||||||
Function / homology | Function and homology information leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production / Antimicrobial peptides / cytokine binding / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / neutrophil-mediated killing of gram-negative bacterium / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / transcription repressor complex / phagocytic vesicle / Degradation of the extracellular matrix / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / protein catabolic process / negative regulation of inflammatory response / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / azurophil granule lumen / positive regulation of immune response / peptidase activity / heparin binding / collagen-containing extracellular matrix / endopeptidase activity / protease binding / response to lipopolysaccharide / defense response to bacterium / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of transcription by RNA polymerase II / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | HOMO SAPIENS (human) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||||||||
Authors | Bode, W. / Wei, A-Z. | ||||||||||||
Citation | Journal: FEBS Lett. / Year: 1988 Title: The refined 2.3 A crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor. Authors: Wei, A.Z. / Mayr, I. / Bode, W. #1: Journal: Embo J. / Year: 1986 Title: X-Ray Crystal Structure of the Complex of Human Leukocyte Elastase (Pmn Elastase) and the Third Domain of the Turkey Ovomucoid Inhibitor Authors: Bode, W. / Wei, A.-Z. / Huber, R. / Meyer, E. / Travis, J. / Neumann, S. | ||||||||||||
History |
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Remark 700 | SHEET THE SHEETS PRESENTED AS *B1* AND *B2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *B1* AND *B2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ppg.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ppg.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ppg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ppg_validation.pdf.gz | 573.5 KB | Display | wwPDB validaton report |
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Full document | 1ppg_full_validation.pdf.gz | 592.7 KB | Display | |
Data in XML | 1ppg_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1ppg_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/1ppg ftp://data.pdbj.org/pub/pdb/validation_reports/pp/1ppg | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23318.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P08246, leukocyte elastase |
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#2: Protein/peptide | |
#3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1- ...alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Water | ChemComp-HOH / |
Compound details | THE UNBOUND FORM OF THE INHIBITOR IS MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE. UPON REACTION ...THE UNBOUND FORM OF THE INHIBITOR IS MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETH |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 9 / Method: vapor diffusion, hanging drop | |||||||||||||||
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: 2.3 Å / Num. obs: 7390 / % possible obs: 75 % / Num. measured all: 20260 / Rmerge(I) obs: 0.081 |
-Processing
Software | Name: EREF / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.3→8 Å / Rfactor Rwork: 0.145 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Software | *PLUS Name: EREF / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Num. reflection obs: 7104 / σ(I): 2 / Rfactor obs: 0.145 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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