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- PDB-1zs0: Crystal structure of the complex between MMP-8 and a phosphonate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zs0 | ||||||
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Title | Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (S-enantiomer) | ||||||
![]() | Neutrophil collagenase | ||||||
![]() | HYDROLASE / phosphonic inhibitor / sulphonamide junction / stereoselective inhibition | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Pochetti, G. / Gavuzzo, E. / Campestre, C. / Agamennone, M. / Tortorella, P. / Consalvi, V. / Gallina, C. / Hiller, O. / Tschesche, H. / Tucker, P.A. / Mazza, F. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() Title: X-ray structures of 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56 KB | Display | ![]() |
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PDB format | ![]() | 37.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 706.3 KB | Display | ![]() |
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Full document | ![]() | 712.6 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zvxC ![]() 1i76S 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 250 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EIN.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EIN.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EIN / ( | #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG6000, MES/NaOH, NaCl, CaCl2, ZnCl2, Na Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8042 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→30 Å / Num. all: 21703 / Num. obs: 21073 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 5 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 9.1 / % possible all: 90.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1I76 Resolution: 1.56→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.56→10 Å
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Refine LS restraints |
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