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Open data
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Basic information
Entry | Database: PDB / ID: 1b0f | |||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL ELASTASE WITH MDL 101, 146 | |||||||||
![]() | PROTEIN (ELASTASE) | |||||||||
![]() | HYDROLASE / SERINE PROTEASE / FLUOROETHYL KETONES | |||||||||
Function / homology | ![]() 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 / 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 / positive regulation of immune response / azurophil granule lumen / heparin binding / peptidase activity / protease binding / collagen-containing extracellular matrix / endopeptidase activity / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Schreuder, H.A. / Metz, W.A. / Peet, N.P. / Pelton, J.T. / Tardif, C. | |||||||||
![]() | ![]() Title: Inhibition of human neutrophil elastase. 4. Design, synthesis, X-ray crystallographic analysis, and structure-activity relationships for a series of P2-modified, orally active peptidyl pentafluoroethyl ketones. Authors: Cregge, R.J. / Durham, S.L. / Farr, R.A. / Gallion, S.L. / Hare, C.M. / Hoffman, R.V. / Janusz, M.J. / Kim, H.O. / Koehl, J.R. / Mehdi, S. / Metz, W.A. / Peet, N.P. / Pelton, J.T. / ...Authors: Cregge, R.J. / Durham, S.L. / Farr, R.A. / Gallion, S.L. / Hare, C.M. / Hoffman, R.V. / Janusz, M.J. / Kim, H.O. / Koehl, J.R. / Mehdi, S. / Metz, W.A. / Peet, N.P. / Pelton, J.T. / Schreuder, H.A. / Sunder, S. / Tardif, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.2 KB | Display | ![]() |
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PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1b0eC ![]() 1hneS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23233.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-SEI / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 63.31 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 3.8 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 19, 1993 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 6729 / % possible obs: 99.1 % / Redundancy: 7.2 % / Rsym value: 0.099 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 5.2 % / Rsym value: 0.371 / % possible all: 95.9 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Redundancy: 7.2 % / Num. measured all: 48509 / Rmerge(I) obs: 0.099 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å / Redundancy: 5.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HNE Resolution: 3→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Displacement parameters | Biso mean: 21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.13 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.206 |