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- PDB-5h0u: Crystal structure of the catalytic domain of membrane type 1 matr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h0u | ||||||
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Title | Crystal structure of the catalytic domain of membrane type 1 matrix metalloproteinase | ||||||
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![]() | HYDROLASE / catalytic domain membrane type 1 matrix metalloproteinase MT1-MMP | ||||||
Function / homology | ![]() membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / head development / chondrocyte proliferation / astrocyte cell migration / response to odorant / tissue remodeling ...membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / head development / chondrocyte proliferation / astrocyte cell migration / response to odorant / tissue remodeling / negative regulation of focal adhesion assembly / positive regulation of protein processing / endochondral ossification / embryonic cranial skeleton morphogenesis / zymogen activation / endothelial cell proliferation / intermediate filament cytoskeleton / positive regulation of B cell differentiation / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / negative regulation of Notch signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / metalloaminopeptidase activity / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / regulation of protein localization to plasma membrane / response to mechanical stimulus / ovarian follicle development / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / skeletal system development / cell motility / lung development / protein catabolic process / response to organic cyclic compound / protein processing / metalloendopeptidase activity / Golgi lumen / response to estrogen / male gonad development / melanosome / integrin binding / cytoplasmic vesicle / positive regulation of cell growth / angiogenesis / endopeptidase activity / response to oxidative stress / response to hypoxia / positive regulation of cell migration / serine-type endopeptidase activity / focal adhesion / proteolysis / extracellular space / zinc ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() unidentified (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ogata, H. / Decaneto, E. / Lubitz, W. | ||||||
![]() | ![]() Title: Solvent water interactions within the active site of the membrane type I matrix metalloproteinase. Authors: Decaneto, E. / Vasilevskaya, T. / Kutin, Y. / Ogata, H. / Grossman, M. / Sagi, I. / Havenith, M. / Lubitz, W. / Thiel, W. / Cox, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.6 KB | Display | ![]() |
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PDB format | ![]() | 38.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bqqS S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 19338.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P50281, membrane-type matrix metalloproteinase-1 |
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#2: Protein/peptide | Mass: 846.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: His-tag / Source: (gene. exp.) unidentified (others) / Production host: ![]() ![]() |
-Non-polymers , 5 types, 82 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EPE / | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Ammonium nitrate, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.239→44.544 Å / Num. obs: 12491 / % possible obs: 99.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.239→2.37 Å / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BQQ Resolution: 2.239→44.544 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.239→44.544 Å
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Refine LS restraints |
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LS refinement shell |
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