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Yorodumi- PDB-5a09: Crystal Structure of human neutrophil elastase in complex with a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a09 | |||||||||
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Title | Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor | |||||||||
Components | NEUTROPHIL ELASTASE | |||||||||
Keywords | HYDROLASE / TRYPSIN FAMILY FOLD / PROTEASE / 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 / acute inflammatory response to antigenic stimulus / negative regulation of chemotaxis / 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 / acute inflammatory response to antigenic stimulus / negative regulation of chemotaxis / 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 / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / neutrophil-mediated killing of gram-negative bacterium / cytokine binding / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / phagocytic vesicle / transcription repressor complex / Degradation of the extracellular matrix / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / negative regulation of inflammatory response / protein catabolic process / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / positive regulation of immune response / azurophil granule lumen / heparin binding / peptidase activity / endopeptidase activity / protease binding / collagen-containing extracellular matrix / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | |||||||||
Authors | vonNussbaum, F. / Li, V.M.-J. / Allerheiligen, S. / Anlauf, S. / Baerfacker, L. / Bechem, M. / Delbeck, M. / Fitzgerald, M.F. / Gerisch, M. / Gielen-Haertwig, H. ...vonNussbaum, F. / Li, V.M.-J. / Allerheiligen, S. / Anlauf, S. / Baerfacker, L. / Bechem, M. / Delbeck, M. / Fitzgerald, M.F. / Gerisch, M. / Gielen-Haertwig, H. / Haning, H. / Karthaus, D. / Lang, D. / Lustig, K. / Meibom, D. / Mittendorf, J. / Rosentreter, U. / Schaefer, M. / Schaefer, S. / Schamberger, J. / Telan, L.A. / Tersteegen, A. | |||||||||
Citation | Journal: ChemMedChem / Year: 2015 Title: Freezing the Bioactive Conformation to Boost Potency: The Identification of BAY 85-8501, a Selective and Potent Inhibitor of Human Neutrophil Elastase for Pulmonary Diseases. Authors: von Nussbaum, F. / Li, V.M. / Allerheiligen, S. / Anlauf, S. / Barfacker, L. / Bechem, M. / Delbeck, M. / Fitzgerald, M.F. / Gerisch, M. / Gielen-Haertwig, H. / Haning, H. / Karthaus, D. / ...Authors: von Nussbaum, F. / Li, V.M. / Allerheiligen, S. / Anlauf, S. / Barfacker, L. / Bechem, M. / Delbeck, M. / Fitzgerald, M.F. / Gerisch, M. / Gielen-Haertwig, H. / Haning, H. / Karthaus, D. / Lang, D. / Lustig, K. / Meibom, D. / Mittendorf, J. / Rosentreter, U. / Schafer, M. / Schafer, S. / Schamberger, J. / Telan, L.A. / Tersteegen, A. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET 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 | 5a09.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a09.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 5a09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a09_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5a09_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5a09_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 5a09_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a09 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a09 | HTTPS FTP |
-Related structure data
Related structure data | 5a0aC 5a0bC 5a0cC 1ppgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23318.982 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-247 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P08246, leukocyte elastase | ||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / | #4: Chemical | ChemComp-JJD / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.1 % / Description: NONE |
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Crystal grow | Details: 28%PEG4000, 0.1MTRIS/HCL AT PH 8.2, 0.7MLICL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→63.25 Å / % possible obs: 96.4 % / Observed criterion σ(I): 1.1 / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 1.81→1.9 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.1 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PPG Resolution: 1.81→63.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.815 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.866 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→63.25 Å
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Refine LS restraints |
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