+Open data
-Basic information
Entry | Database: PDB / ID: 3lik | ||||||
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Title | Human MMP12 in complex with non-zinc chelating inhibitor | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / MMP12 elastase non-chelating inhibitor / HYDROLASE / 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 / rigid body / Resolution: 1.8 Å | ||||||
Authors | Stura, E.A. / Dive, V. / Devel, L. / Czarny, B. / Vera, L. / Beau, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Insights from selective non-phosphinic inhibitors of MMP-12 tailored to fit with an S1' loop canonical conformation. Authors: Devel, L. / Garcia, S. / Czarny, B. / Beau, F. / LaJeunesse, E. / Vera, L. / Georgiadis, D. / Stura, E. / Dive, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lik.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lik.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 3lik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lik_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3lik_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3lik_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3lik_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/3lik ftp://data.pdbj.org/pub/pdb/validation_reports/li/3lik | HTTPS FTP |
-Related structure data
Related structure data | 3lilC 3lirC 3ljgC 1rmzS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17615.670 Da / Num. of mol.: 1 / Fragment: MMP-12 catalitic subunit (RESIDUES 106-263) / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P39900, macrophage elastase |
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-Non-polymers , 6 types, 189 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EEG / | #5: Chemical | ChemComp-HAE / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MMP12 at 4mg/ml co-crystallization with AHA and non-chelating inhibitor with precipitant: 25% PEG 10K, 100mM NaCl,0.2M imidazole malate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-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 4r / Detector: CCD / Date: Apr 15, 2009 / Details: mirrors |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.27 Å / Num. all: 15104 / Num. obs: 13458 / % possible obs: 89.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.08 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15.23 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1719 / Rsym value: 0.309 / % possible all: 79.7 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body Starting model: PDB ENTRY 1RMZ Resolution: 1.8→46.295 Å / SU ML: 0.16 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / 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 / Bsol: 47.345 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.746 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.295 Å
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Refine LS restraints |
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LS refinement shell |
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