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Yorodumi- PDB-4wzv: Crystal structure of a hydroxamate based inhibitor EN140 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wzv | ||||||
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Title | Crystal structure of a hydroxamate based inhibitor EN140 in complex with the MMP-9 catalytic domain | ||||||
Components | Matrix metalloproteinase-9,Matrix metalloproteinase-9 | ||||||
Keywords | HYDROLASE / MMP9 Inhibitor complex / Thyroid hormone-binding protein | ||||||
Function / homology | Function and homology information 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 / positive regulation of DNA binding ...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 / positive regulation of DNA binding / 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 / cellular response to cadmium ion / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / cellular response to reactive oxygen species / Signaling by SCF-KIT / metalloendopeptidase activity / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / endopeptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / Extra-nuclear estrogen signaling / ficolin-1-rich granule lumen / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Stura, E.A. / Vera, L. / Cassar-Lajeunesse, E. / Nuti, E. / Dive, V. / Rossello, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: N-O-Isopropyl Sulfonamido-Based Hydroxamates as Matrix Metalloproteinase Inhibitors: Hit Selection and in Vivo Antiangiogenic Activity. Authors: Nuti, E. / Cantelmo, A.R. / Gallo, C. / Bruno, A. / Bassani, B. / Camodeca, C. / Tuccinardi, T. / Vera, L. / Orlandini, E. / Nencetti, S. / Stura, E.A. / Martinelli, A. / Dive, V. / Albini, A. / Rossello, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wzv.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wzv.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wzv_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4wzv_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4wzv_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 4wzv_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/4wzv ftp://data.pdbj.org/pub/pdb/validation_reports/wz/4wzv | HTTPS FTP |
-Related structure data
Related structure data | 4xctC 4h3xS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17904.859 Da / Num. of mol.: 2 Fragment: catalytic domain, UNP residues 110-216,catalytic domain, UNP residues 392-444 Source method: isolated from a genetically manipulated source Details: E40 is a ligand. 7 residues have been cleaved. unp residues 110-214 and 391-444 Source: (gene. exp.) Homo sapiens (human) / Gene: MMP9, CLG4B / Production host: Escherichia coli (E. coli) / References: UniProt: P14780, gelatinase B |
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-Non-polymers , 10 types, 659 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CA / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-AZI / | #9: Chemical | ChemComp-NA / #10: Chemical | ChemComp-GOL / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.31 % / Description: long prismatic crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.25 Details: protein: 5mg/mL hMMP9-WT with 120 milli-M acetohydroxamic acid. Reservoir: 36% MPEG 5K, 90mM bicine, pH 7.25. Cryoprotectant: 40% MPEG 5K, 5% Di-ethyleneglycol, 10% AAB buffer, pH 8.0 PH range: 7.25-8.0 / Temp details: cooled incubator |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 24, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 38771 / Num. obs: 38365 / % possible obs: 99 % / Redundancy: 4.17 % / Biso Wilson estimate: 21.971 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.144 / Net I/σ(I): 8.41 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 3.92 % / Rmerge(I) obs: 1.339 / Mean I/σ(I) obs: 1.19 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H3X Resolution: 1.65→42.126 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→42.126 Å
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Refine LS restraints |
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LS refinement shell |
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