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- PDB-1ycm: Solution Structure of matrix metalloproteinase 12 (MMP12) in the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ycm | ||||||
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Title | Solution Structure of matrix metalloproteinase 12 (MMP12) in the presence of N-Isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH) | ||||||
![]() | Macrophage metalloelastase | ||||||
![]() | HYDROLASE / macrophage metalloelastase / MMP-12 / solution structure / NNGH / zinc / calcium / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
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 | SOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics, residue dipolar couplings | ||||||
![]() | Bertini, I. / Calderone, V. / Cosenza, M. / Fragai, M. / Lee, Y.M. / Luchinat, C. / Mangani, S. / Terni, B. / Turano, P. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() Title: Conformational variability of matrix metalloproteinases: Beyond a single 3D structure. Authors: Bertini, I. / Calderone, V. / Cosenza, M. / Fragai, M. / Lee, Y.M. / Luchinat, C. / Mangani, S. / Terni, B. / Turano, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 911.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 446 KB | Display | ![]() |
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Full document | ![]() | 615 KB | Display | |
Data in XML | ![]() | 83.1 KB | Display | |
Data in CIF | ![]() | 98.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rmzC ![]() 1y93C ![]() 1z3jC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 17615.670 Da / Num. of mol.: 1 / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NGH / | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using distance, dihedral angle and H-bond restraints with residue dipolar coupling restraints |
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Sample preparation
Details | Contents: 0.9 mM MMP12 U-15N,13C; 10 mM deuterated Tris, 5 mM CaCl2, 0.1 mM ZnCl2, 0.3 M NaCl; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 0.3 M NaCl / pH: 7.2 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, torsion angle dynamics, residue dipolar couplings Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |