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Open data
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Basic information
Entry | Database: PDB / ID: 1os2 | ||||||
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Title | Ternary enzyme-product-inhibitor complexes of human MMP12 | ||||||
![]() | Macrophage metalloelastase | ||||||
![]() | HYDROLASE / MATRIX METALLOPROTEINASE / HYDROXAMIC ACID / MMP12 / ELASTASE / COMPLEX (ELASTASE-INHIBITOR) / METALLO ELASTASE | ||||||
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 / positive regulation of interferon-alpha production / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Mangani, S. / Terni, B. | ||||||
![]() | ![]() Title: X-ray Structures of Binary and Ternary Enzyme-Product-Inhibitor Complexes of Matrix Metalloproteinases Authors: Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Mangani, S. / Terni, B. #1: ![]() Title: Substrate specificity determinants of human macrophage elastase (MMP-12) based on the 1.1 A crystal structure Authors: Lang, R. / Kocourek, A. / Braun, M. / Tschesche, H. / Huber, R. / Bode, W. / Maskos, K. | ||||||
History |
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Remark 600 | HET GROUP TRIVIAL NAME: HAE IS ALSO KNOWN AS ACETOHYDROXAMIC ACID |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217.9 KB | Display | ![]() |
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PDB format | ![]() | 173.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1os9C ![]() 1jk3S 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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Details | The protein is monomeric in vivo, while there are six molecules in the crystal asymmetric unit. |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 18331.467 Da / Num. of mol.: 6 / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 344 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HAE.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HAE.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.28 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Tris, PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 9, 2002 / Details: Si (111) mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9322 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→107 Å / Num. all: 64964 / Num. obs: 64964 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 1.9 / Num. unique all: 9418 / Rsym value: 0.078 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 107 Å / % possible obs: 100 % / Num. measured all: 471410 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.076 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JK3 Resolution: 2.15→69.01 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.871 / SU ML: 0.153 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.244 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.148 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→69.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Num. reflection all: 64964 / Lowest resolution: 19.8 Å / Num. reflection Rfree: 3250 / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.21 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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