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- PDB-4hma: Crystal structure of an MMP twin carboxylate based inhibitor LC20... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hma | ||||||
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Title | Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the MMP-9 catalytic domain | ||||||
![]() | Matrix metalloproteinase-9 | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / HYDROLASE/TWIN INHIBITOR / Zincin-like / Gelatinase / Collagenase (Catalytic Domain) / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | ![]() gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / cellular response to cadmium ion / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stura, E.A. / Antoni, C. / Vera, L. / Nuti, E. / Carafa, L. / Cassar-Lajeunesse, E. / Dive, V. / Rossello, A. | ||||||
![]() | ![]() Title: Crystallization of bi-functional ligand protein complexes. Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2005 Title: A new development of matrix metalloproteinase inhibitors: twin hydroxamic acids as potent inhibitors of MMPs. Authors: Rossello, A. / Nuti, E. / Catalani, M.P. / Carelli, P. / Orlandini, E. / Rapposelli, S. / Tuccinardi, T. / Atkinson, S.J. / Murphy, G. / Balsamo, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.6 KB | Display | ![]() |
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PDB format | ![]() | 72.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 859.9 KB | Display | ![]() |
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Full document | ![]() | 874 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h1qC ![]() 4h2eC ![]() 4h30C ![]() 4h3xC ![]() 4h49C ![]() 4h76C ![]() 4h82SC ![]() 4h84C ![]() 4i03C C: citing same article ( S: Starting model for refinement |
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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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Details | THE TWIN INHIBITOR 0Z CAUSE THE ENZYME TO FORM A DIMER |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17932.871 Da / Num. of mol.: 2 / Fragment: MMP-9 catalytic domain 107-215,391-443 / Mutation: V391Q E402Q Source method: isolated from a genetically manipulated source Details: construct: 110 216 and 392 444 Mutagenesis: Glu402Gln Structure: renumbered omi tting missing domain. Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 375 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/0ZD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MLT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/0ZD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MLT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-0ZD / | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PGO / #7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-MLT / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Protein: human MMP9 (E402Q) at 308.7 micro-M twin inhibitor LC20 at 154 micro-M (stoichiometry 2:1) and 120mM acetohydroxamic acid. RESERVOIR: 12% Polyethylene glycol 20,000, 1.5M NaCl, 0.1 ...Details: Protein: human MMP9 (E402Q) at 308.7 micro-M twin inhibitor LC20 at 154 micro-M (stoichiometry 2:1) and 120mM acetohydroxamic acid. RESERVOIR: 12% Polyethylene glycol 20,000, 1.5M NaCl, 0.1 M PCTP (Na propionate, Na cacodylate, Bis-Tris-propane ratio 2:1:2; 75% pH 4, 25% pH 9.5) CRYOPROTECTANT: 40% C2 (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol), 9% PEG 10,000 1.5M NaCl, 0.1M PCTP 80/2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2012 / Details: bent cylindrical mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→50 Å / Num. all: 26173 / Num. obs: 26019 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.98 % / Biso Wilson estimate: 36.556 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.155 / Net I/σ(I): 8.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4H82 Resolution: 1.94→42.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.156 / SU ML: 0.145 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.212 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.048 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→42.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.943→1.993 Å / Total num. of bins used: 20
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