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Yorodumi- PDB-2k2g: Solution structure of the wild-type catalytic domain of human mat... -
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-Basic information
Entry | Database: PDB / ID: 2k2g | ||||||
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Title | Solution structure of the wild-type catalytic domain of human matrix metalloproteinase 12 (MMP-12) in complex with a tight-binding inhibitor | ||||||
Components | Macrophage metalloelastase | ||||||
Keywords | HYDROLASE / macrophage elastase / matrix metalloproteinase / protein-ligand structure / catalytic domain / human gene / Calcium / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen | ||||||
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 / lung alveolus development / negative regulation of type I interferon-mediated signaling pathway ...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 / lung alveolus development / negative regulation of type I interferon-mediated signaling pathway / positive regulation of interferon-alpha production / response to amyloid-beta / 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 | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing | ||||||
Model details | ensemble of 17 structures | ||||||
Authors | Markus, M.A. / Dwyer, B. / Wolfrom, S. / Li, J. / Li, W. / Malakian, K. / Wilhelm, J. / Tsao, D.H.H. | ||||||
Citation | Journal: J.Biomol.Nmr / Year: 2008 Title: Solution structure of wild-type human matrix metalloproteinase 12 (MMP-12) in complex with a tight-binding inhibitor. Authors: Markus, M.A. / Dwyer, B. / Wolfrom, S. / Li, J. / Li, W. / Malakian, K. / Wilhelm, J. / Tsao, D.H. #1: Journal: J.Biomol.NMR / Year: 2005 Title: 1H, 13C, and 15N assignments of MMP-12, a key protease implicated in lung tissue remodeling Authors: Markus, M.A. / Dwyer, B. / Wolfrom, S. / Li, J. / Li, W. / Malakian, K. / Wilhelm, J. / Tsao, D.H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k2g.cif.gz | 863.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k2g.ent.gz | 726 KB | Display | PDB format |
PDBx/mmJSON format | 2k2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k2g_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 2k2g_full_validation.pdf.gz | 613.3 KB | Display | |
Data in XML | 2k2g_validation.xml.gz | 77.8 KB | Display | |
Data in CIF | 2k2g_validation.cif.gz | 93.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/2k2g ftp://data.pdbj.org/pub/pdb/validation_reports/k2/2k2g | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18366.605 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP residues 100 to 263) 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(DE3) / References: UniProt: P39900, macrophage elastase | ||
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#2: Chemical | #3: Chemical | ChemComp-DSV / | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: ensemble of 17 structures | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Chemical shift assignments were previously reported, so experiments to support the assignments will not be described. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 160 / pH: 6 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing, simulated annealing Software ordinal: 1 Details: for structures with NOE and angle restraints, to incorporate dipolar couplings | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 17 |