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Yorodumi- PDB-3dng: Crystal structure of the complex between MMP-8 and a non-zinc che... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dng | ||||||
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Title | Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor | ||||||
Components | Neutrophil collagenase | ||||||
Keywords | HYDROLASE / selective inhibition / non-zinc chelating inhibitors / Calcium / Collagen degradation / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen | ||||||
Function / homology | Function and homology information 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 / endopeptidase activity / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pochetti, G. / Montanari, R. / Mazza, F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Extra Binding Region Induced by Non-Zinc Chelating Inhibitors into the S(1)' Subsite of Matrix Metalloproteinase 8 (MMP-8) Authors: Pochetti, G. / Montanari, R. / Gege, C. / Chevrier, C. / Taveras, A.G. / Mazza, F. #1: Journal: Chem.Biol. / Year: 2005 Title: Structural basis for the highly selective inhibition of MMP-13 Authors: Engel, C.K. / Pirard, B. / Schimanski, S. / Kirsch, R. / Habermann, J. / Klingler, O. / Schlotte, V. / Weithmann, K.U. / Wendt, K.U. #2: Journal: J.Biol.Chem. / Year: 2007 Title: Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia side effects Authors: Johnson, A.R. / Pavlovsky, A.G. / Ortwine, D.F. / Prior, F. / Man, C.F. / Bornemeier, D.A. / Banotai, C.A. / Mueller, W.T. / McConnell, P. / Yan, C. / Baragi, V. / Lesch, C. / Roark, W.H. / ...Authors: Johnson, A.R. / Pavlovsky, A.G. / Ortwine, D.F. / Prior, F. / Man, C.F. / Bornemeier, D.A. / Banotai, C.A. / Mueller, W.T. / McConnell, P. / Yan, C. / Baragi, V. / Lesch, C. / Roark, W.H. / Wilson, M. / Datta, K. / Guzman, R. / Han, H.K. / Dyer, R.D. #3: Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structures of novel non-peptidic, non-zinc chelating inhibitors bound to MMP-12 Authors: Morales, R. / Perrier, S. / Florent, J.M. / Beltra, J. / Dufour, S. / De Mendez, I. / Manceau, P. / Tertre, A. / Moreau, F. / Compere, D. / Dublanchet, A.C. / O'Gara, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dng.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dng.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 3dng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dng_validation.pdf.gz | 941.6 KB | Display | wwPDB validaton report |
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Full document | 3dng_full_validation.pdf.gz | 953.8 KB | Display | |
Data in XML | 3dng_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3dng_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/3dng ftp://data.pdbj.org/pub/pdb/validation_reports/dn/3dng | HTTPS FTP |
-Related structure data
Related structure data | 3dpeC 3dpfC 1i76S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18111.744 Da / Num. of mol.: 2 / Fragment: MMP-8 catalytic domain, UNP residues 100-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP8, CLG1 / Plasmid: pSVB30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22894, neutrophil collagenase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Hanging droplets were made by mixing 1.5-3.0ml of protein/inhibitor solution with 5ml of PEG solution (10% PEG6000, 0.2M Mes-NaOH, 0.02% NaN3, pH6.0). Droplets were concentrated against a ...Details: Hanging droplets were made by mixing 1.5-3.0ml of protein/inhibitor solution with 5ml of PEG solution (10% PEG6000, 0.2M Mes-NaOH, 0.02% NaN3, pH6.0). Droplets were concentrated against a reservoir buffer containing 1.0-2.0M sodium phosphate, 0.02% NaN3, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2007 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 20603 / Num. obs: 20603 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 3.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I76 Resolution: 2→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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