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- PDB-5d3c: Crystal structure of a double mutant catalytic domain of Human MM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d3c | ||||||
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Title | Crystal structure of a double mutant catalytic domain of Human MMP12 in complex with an hydroxamate analogue of RXP470 | ||||||
![]() | Macrophage metalloelastase | ||||||
![]() | HYDROLASE / MMP12 / Human / Macrophage MetalloElastase / RXP470 / hydroxamate | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rouanet-Mehouas, C. / Devel, L. / Dive, V. / Stura, E.A. | ||||||
![]() | ![]() Title: Zinc-Metalloproteinase Inhibitors: Evaluation of the Complex Role Played by the Zinc-Binding Group on Potency and Selectivity. Authors: Rouanet-Mehouas, C. / Czarny, B. / Beau, F. / Cassar-Lajeunesse, E. / Stura, E.A. / Dive, V. / Devel, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.8 KB | Display | ![]() |
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PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739 KB | Display | ![]() |
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Full document | ![]() | 739.3 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cxaC ![]() 5czmC ![]() 5d2bC ![]() 4gqlS S: Starting model for refinement C: citing same article ( |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17557.568 Da / Num. of mol.: 1 / Fragment: UNP residues 106-263 / Mutation: F171D K241A Source method: isolated from a genetically manipulated source Details: MMP12 F171D K141A mutant for calorimetric studies Catalytic domain (UNP residues 106-263) Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-56O / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.38 % / Description: long prismatic crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: Protein : MMP12 F67D K241A, 1 mili-M + 10 mili-M AHA Drop : 1 micro-L protein + 0.2 micro-L inhibitor (5 mili-M in DMSO) Precipitant : 20% PEG4000, 0.2 M TRIS pH 9.5 Cryoprotectant : 10 % ...Details: Protein : MMP12 F67D K241A, 1 mili-M + 10 mili-M AHA Drop : 1 micro-L protein + 0.2 micro-L inhibitor (5 mili-M in DMSO) Precipitant : 20% PEG4000, 0.2 M TRIS pH 9.5 Cryoprotectant : 10 % diethylene glycol + 5 % glycerol + 10 % 2,3-butanediol + 5 % 1,4-dioxane +25% PEG6000,+ 100 mili-M TRIS HCl, pH 8. PH range: 8.0-9.5 / Temp details: cooled incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: N2 stream |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2015 Details: convex horizontal pre-focussing mirror (HPM) and a pair of focusing bimorph mirrors in Kirkpatrick-Baez (KB) configuration |
Radiation | Monochromator: cryogenically cooled channel-cut Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→46.438 Å / Num. all: 72969 / Num. obs: 71186 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.83 % / Rmerge(I) obs: 0.123 / Rsym value: 0.121 / Net I/σ(I): 9.47 |
Reflection shell | Resolution: 1.31→1.35 Å / Redundancy: 3.93 % / Rmerge(I) obs: 1.64 / Mean I/σ(I) obs: 1.03 / % possible all: 73.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GQL Resolution: 1.314→46.438 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 20.63 / 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: 1.314→46.438 Å
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Refine LS restraints |
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LS refinement shell |
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