+Open data
-Basic information
Entry | Database: PDB / ID: 4ja1 | ||||||
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Title | Structure of MMP3 complexed with a platinum-based inhibitor | ||||||
Components | Stromelysin-1 | ||||||
Keywords | hydrolase/hydrolase inhibitor / Matrix metalloprotease / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell migration / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to amino acid stimulus / protein catabolic process / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Belviso, B.D. / Arnesano, F. / Calderone, V. / Caliandro, R. / Natile, G. / Siliqi, D. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2013 Title: Structure of matrix metalloproteinase-3 with a platinum-based inhibitor. Authors: Belviso, B.D. / Caliandro, R. / Siliqi, D. / Calderone, V. / Arnesano, F. / Natile, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ja1.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ja1.ent.gz | 116.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ja1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ja1_validation.pdf.gz | 753.5 KB | Display | wwPDB validaton report |
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Full document | 4ja1_full_validation.pdf.gz | 762.7 KB | Display | |
Data in XML | 4ja1_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 4ja1_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/4ja1 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/4ja1 | HTTPS FTP |
-Related structure data
Related structure data | 4dpeC 4g9lC 1slnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19416.529 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP3, STMY1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08254, stromelysin 1 |
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-Non-polymers , 6 types, 126 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-NGH / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein 7-15mg/ml, 25-30% (w/v) PEG 8000, 10 mM CaCl2, 100 mM TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å | ||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2011 | ||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||
Reflection | Resolution: 1.96→34.22 Å / Num. obs: 21159 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SLN Resolution: 1.96→34.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||
Displacement parameters | Biso mean: 26.438 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→34.22 Å
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LS refinement shell | Resolution: 1.96→2.011 Å / Total num. of bins used: 20
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