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Yorodumi- PDB-1zvx: Crystal structure of the complex between MMP-8 and a phosphonate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zvx | ||||||
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Title | Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (R-enantiomer) | ||||||
Components | Neutrophil collagenase | ||||||
Keywords | HYDROLASE / stereoselective inhibition / phosphonic inhibitors / sulfonamide junction | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Pochetti, G. / Gavuzzo, E. / Campestre, C. / Agamennone, M. / Tortorella, P. / Consalvi, V. / Gallina, C. / Hiller, O. / Tschesche, H. / Tucker, P.A. / Mazza, F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Structural insight into the stereoselective inhibition of MMP-8 by enantiomeric sulfonamide phosphonates. Authors: Pochetti, G. / Gavuzzo, E. / Campestre, C. / Agamennone, M. / Tortorella, P. / Consalvi, V. / Gallina, C. / Hiller, O. / Tschesche, H. / Tucker, P.A. / Mazza, F. #1: Journal: Protein Sci. / Year: 1999 Title: X-ray structure of human stromelysin catalytic domain complexed with nonpeptide inhibitors: implications for inhibitor selectivity Authors: Pavlovsky, A.G. / Williams, M.G. / Ye, Q.Z. / Ortwine, D.F. / Purchase II, C.F. / White, A.D. / Dhanaraj, V. / Roth, B.D. / Johnson, L.L. / Hupe, D. / Humblet, C. / Blundell, T.L. #2: Journal: J.Med.Chem. / Year: 2000 Title: Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design Authors: Gavuzzo, E. / Pochetti, G. / Mazza, F. / Gallina, C. / Gorini, B. / D'Alessio, S. / Pieper, M. / Tschesche, H. / Tucker, P.A. #3: Journal: Eur.J.Biochem. / Year: 1995 Title: X-ray structuresof human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design Authors: Grams, F. / Reinemer, P. / Powers, J.C. / Kleine, T. / Pieper, M. / Tschesche, H. / Huber, R. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zvx.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zvx.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zvx_validation.pdf.gz | 663.9 KB | Display | wwPDB validaton report |
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Full document | 1zvx_full_validation.pdf.gz | 670.2 KB | Display | |
Data in XML | 1zvx_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1zvx_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/1zvx ftp://data.pdbj.org/pub/pdb/validation_reports/zv/1zvx | HTTPS FTP |
-Related structure data
Related structure data | 1zs0C 1i76S 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: 18111.744 Da / Num. of mol.: 1 Fragment: catalytic domain of neutrophil collagenase (Residues:80-242) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP8, CLG1 / Plasmid: pSVB30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22894, neutrophil collagenase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FIN / ( | #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: 1.6 Å3/Da / Density % sol: 24.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG6000, MES/NaOH, NaCl, CaCl2, ZnCl2, NaPhosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8042 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 28, 2004 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8042 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→30 Å / Num. all: 10210 / Num. obs: 10210 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.9 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I76 Resolution: 1.87→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.87→10 Å
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