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Yorodumi- PDB-3nx7: Crystal structure of the catalytic domain of human MMP12 complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nx7 | ||||||
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Title | Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor N-Hydroxy-2-(N-(2-hydroxyethyl)4-methoxyphenylsulfonamido)acetamide | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | HYDROLASE / MATRIX METALLOPROTEINASE / MMP12 / ELASTASE / COMPLEX (ELASTASE-INHIBITOR) | ||||||
Function / homology | Function and homology information macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / lung alveolus development / negative regulation of type I interferon-mediated signaling pathway ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / lung alveolus development / negative regulation of type I interferon-mediated signaling pathway / positive regulation of interferon-alpha production / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix / extracellular matrix organization / cellular response to virus / metalloendopeptidase activity / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bertini, I. / Calderone, V. / Fragai, M. / Giachetti, A. / Loconte, M. / Luchinat, C. / Maletta, M. / Nativi, C. / Yeo, K.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Exploring the subtleties of drug-receptor interactions: the case of matrix metalloproteinases Authors: Bertini, I. / Calderone, V. / Fragai, M. / Giachetti, A. / Loconte, M. / Luchinat, C. / Maletta, M. / Nativi, C. / Yeo, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nx7.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nx7.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 3nx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nx7_validation.pdf.gz | 736.7 KB | Display | wwPDB validaton report |
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Full document | 3nx7_full_validation.pdf.gz | 736.7 KB | Display | |
Data in XML | 3nx7_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 3nx7_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/3nx7 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/3nx7 | HTTPS FTP |
-Related structure data
Related structure data | 3f15C 3f16C 3f17C 3f18C 3f19C 3f1aC 3lk8C 1y93S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17484.475 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN (UNP residues 106 to 263) / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HME, MMP12 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P39900, macrophage elastase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #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: 2.17 Å3/Da / Density % sol: 43.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M TRIS, 30% PEG 6000, PH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: May 12, 2005 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30.21 Å / Num. all: 13172 / Num. obs: 13172 / % possible obs: 95 % / Redundancy: 3.2 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 1345 / % possible all: 68.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Y93 Resolution: 1.8→30.21 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.329 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R Free: 0.127 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.039 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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