[English] 日本語
Yorodumi- PDB-4guy: Human MMP12 catalytic domain in complex with*N*-Hydroxy-2-(2-(4-m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4guy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human MMP12 catalytic domain in complex with*N*-Hydroxy-2-(2-(4-methoxyphenyl)ethylsulfonamido)acetamide | |||||||||
Components | Macrophage metalloelastase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / MMP-12 / Matrix / metalloproteinase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
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 / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Calderone, V. / Fragai, M. / Luchinat, C. / Massaro, A. / Mordini, A. / Mori, M. | |||||||||
Citation | Journal: To be Published Title: Contribution of free energy of solvation to ligand affinity in new potent MMPs inhibitors. Authors: Mori, M. / Massaro, A. / Calderone, V. / Fragai, M. / Luchinat, C. / Mordini, A. #1: 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. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4guy.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4guy.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 4guy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4guy_validation.pdf.gz | 691.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4guy_full_validation.pdf.gz | 693.4 KB | Display | |
Data in XML | 4guy_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 4guy_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/4guy ftp://data.pdbj.org/pub/pdb/validation_reports/gu/4guy | HTTPS FTP |
-Related structure data
Related structure data | 1y93S S: Starting model for refinement |
---|---|
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: UNP RESIDUES 106-263 / Mutation: F171D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Production host: Escherichia coli (E. coli) / References: UniProt: P39900, macrophage elastase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-KLJ / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.03 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M TRIS-HCL, 30% PEG 6000, 1M LICL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5406 / Wavelength: 1.5406 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Mar 12, 2006 / Details: GRAPHITE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2→30.56 Å / Num. all: 10122 / Num. obs: 10122 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 11.53 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.383 / % possible all: 87.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y93 Resolution: 2→30.56 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.841 / SU B: 7.169 / SU ML: 0.189 / Isotropic thermal model: Isotropic with metals anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 13.6 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30.56 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
|