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Yorodumi- PDB-4gr3: Crystal structure of the catalytic domain of Human MMP12 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gr3 | ||||||
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Title | Crystal structure of the catalytic domain of Human MMP12 in complex with selective phosphinic inhibitor RXP470A | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / potent selective phosphinic inhibitor / METZINCIN / Zinc protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...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 / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / positive regulation of interferon-alpha production / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å | ||||||
Authors | Stura, E.A. / Vera, L. / Beau, F. / Devel, L. / Cassar-Lajeunesse, E. / Dive, V. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Molecular determinants of a selective matrix metalloprotease-12 inhibitor: insights from crystallography and thermodynamic studies. Authors: Czarny, B. / Stura, E.A. / Devel, L. / Vera, L. / Cassar-Lajeunesse, E. / Beau, F. / Calderone, V. / Fragai, M. / Luchinat, C. / Dive, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gr3.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gr3.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 4gr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gr3_validation.pdf.gz | 780.5 KB | Display | wwPDB validaton report |
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Full document | 4gr3_full_validation.pdf.gz | 780.8 KB | Display | |
Data in XML | 4gr3_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 4gr3_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/4gr3 ftp://data.pdbj.org/pub/pdb/validation_reports/gr/4gr3 | HTTPS FTP |
-Related structure data
Related structure data | 4gqlSC 4gr0C 4gr8C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17615.670 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 106-263) / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HME, MMP12 / Plasmid: PET24A / 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 | ChemComp-R45 / | Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 707.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32BrN4O10P References: N-{(2S)-3-[(S)-(4-BROMOPHENYL)(HYDROXY)PHOSPHORYL]-2-[(3-PHENYL-1,2-OXAZOL-5-YL)METHYL]PROPANOYL}-L-ALPHA-GLUTAMYL-L-ALPHA-GLUTAMINE #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: 2.31 Å3/Da / Density % sol: 46.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein: hMMP12(F171D) 643 microM. Reservoir: 18% PEG 10000, 0.2 M imidazole malate pH 8.0. Cryoprotectant: 27% PEG 8000, 15% monomethylPEG 550, 10% glycerol, 0.09 M Tris-HCl, pH 8.0, VAPOR ...Details: Protein: hMMP12(F171D) 643 microM. Reservoir: 18% PEG 10000, 0.2 M imidazole malate pH 8.0. Cryoprotectant: 27% PEG 8000, 15% monomethylPEG 550, 10% glycerol, 0.09 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2009 / Details: Toroidal mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.49→50 Å / Num. all: 27105 / Num. obs: 27049 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 7.9 % / Biso Wilson estimate: 21.514 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.099 / Net I/σ(I): 16.12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GQL Resolution: 1.494→46.565 Å / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Phase error: 21.02 / 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: 1.494→46.565 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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