[English] 日本語
Yorodumi- PDB-3f17: Crystal structure of the catalytic domain of human MMP12 complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f17 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor N-(2-nitroso-2-oxoethyl)biphenyl-4-sulfonamide | |||||||||
Components | Macrophage metalloelastase | |||||||||
Keywords | HYDROLASE / MATRIX METALLOPROTEINASE / MMP12 / ELASTASE / COMPLEX (ELASTASE-INHIBITOR) / METALLO ELASTASE / 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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | |||||||||
Authors | Calderone, V. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Exploring the subtleties of drug-receptor interactions: the case of matrix metalloproteinases. Authors: Bertini, I. / Calderone, V. / Fragai, M. / Giachetti, A. / Loconte, M. / Luchinat, C. / Maletta, M. / Nativi, C. / Yeo, K.J. #1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2003 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. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f17.cif.gz | 87 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f17.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 3f17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f17_validation.pdf.gz | 704.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3f17_full_validation.pdf.gz | 705.7 KB | Display | |
Data in XML | 3f17_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 3f17_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/3f17 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/3f17 | HTTPS FTP |
-Related structure data
Related structure data | 3f15C 3f16C 3f18C 3f19C 3f1aC 3lk8C 3nx7C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17484.475 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 106-263 / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HME, MMP12 / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P39900, macrophage elastase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M TRIS, 30% PEG 6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91677 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2004 / Details: mirrors |
Radiation | Monochromator: Si(311) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91677 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. all: 52343 / Num. obs: 52343 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 7.5 / Num. unique all: 4317 / Rsym value: 0.084 / % possible all: 49.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→19.59 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.883 / SU ML: 0.02 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.04 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.687 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→19.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
|