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- PDB-1jh1: Crystal Structure of MMP-8 complexed with a 6H-1,3,4-thiadiazine ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jh1 | ||||||
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Title | Crystal Structure of MMP-8 complexed with a 6H-1,3,4-thiadiazine derived inhibitor | ||||||
![]() | Matrix Metalloproteinase 8 | ||||||
![]() | HYDROLASE / Collagenase / Inhibitor / thiadiazine | ||||||
Function / homology | ![]() neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly ...neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / specific granule lumen / positive regulation of tumor necrosis factor production / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / endopeptidase activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schroder, J. / Henke, A. / Wenzel, H. / Brandstetter, H. / Stammler, H.G. / Stammler, A. / Pfeiffer, W.D. / Tschesche, H. | ||||||
![]() | ![]() Title: Structure-based design and synthesis of potent matrix metalloproteinase inhibitors derived from a 6H-1,3,4-thiadiazine scaffold. Authors: Schroder, J. / Henke, A. / Wenzel, H. / Brandstetter, H. / Stammler, H.G. / Stammler, A. / Pfeiffer, W.D. / Tschesche, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.6 KB | Display | ![]() |
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PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 643.3 KB | Display | ![]() |
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Full document | ![]() | 646.2 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 17612.115 Da / Num. of mol.: 1 / Fragment: MMP-8 catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-JST / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.46 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M MES, 10% PEG6K, 10mM CaCl2, 100mM NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 6.5 / PH range high: 5.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 275 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 2000 / Details: Monochromator |
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: 2.7→50 Å / Num. all: 4893 / Num. obs: 4174 / % possible obs: 85.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.32 / % possible all: 72.4 |
Reflection | *PLUS Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS Rmerge(I) obs: 0.32 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MMP-8 Resolution: 2.7→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 11.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 50 Å / σ(F): 2 / Rfactor obs: 0.211 / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.211 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 11.3 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.007 |