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- PDB-1d8m: CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A HETEROCYCLE-BASED INHIBITOR -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d8m | ||||||
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Title | CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A HETEROCYCLE-BASED INHIBITOR | ||||||
![]() | STROMELYSIN-1 PRECURSOR | ||||||
![]() | HYDROLASE / MIXED ALPHA BETA STRUCTURE / ZINC PROTEASE / INHIBITED | ||||||
Function / homology | ![]() stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / collagen catabolic process / cellular response to nitric oxide ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / collagen catabolic process / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / extracellular matrix disassembly / EGFR Transactivation by Gastrin / regulation of cell migration / Degradation of the extracellular matrix / extracellular matrix / extracellular matrix organization / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / protein catabolic process / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Pikul, S. / Dunham, K.M. / Almstead, N.G. / De, B. / Natchus, M.G. / Taiwo, Y.O. / Williams, L.E. / Hynd, B.A. / Hsieh, L.C. / Janusz, M.J. ...Pikul, S. / Dunham, K.M. / Almstead, N.G. / De, B. / Natchus, M.G. / Taiwo, Y.O. / Williams, L.E. / Hynd, B.A. / Hsieh, L.C. / Janusz, M.J. / Gu, F. / Mieling, G.E. | ||||||
![]() | ![]() Title: Heterocycle-based MMP inhibitors with P2' substituents. Authors: Pikul, S. / Dunham, K.M. / Almstead, N.G. / De, B. / Natchus, M.G. / Taiwo, Y.O. / Williams, L.E. / Hynd, B.A. / Hsieh, L.C. / Janusz, M.J. / Gu, F. / Mieling, G.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.4 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a monomer constructed from chain A or chain B. |
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Components
#1: Protein | Mass: 19416.529 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-BBH / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 6000, sodium chloride, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 27, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.548 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→40 Å / Num. all: 12205 / Num. obs: 11974 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2.44→2.53 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.198 / Num. unique all: 1009 / % possible all: 83.2 |
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Processing
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Refinement | Resolution: 2.44→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Refinement step | Cycle: LAST / Resolution: 2.44→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.315 / Rfactor Rwork: 0.277 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |