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Yorodumi- PDB-1d5j: CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A THIAZEPINE BASED INHIBITOR. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d5j | ||||||
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Title | CRYSTAL STRUCTURE OF MMP3 COMPLEXED WITH A THIAZEPINE BASED INHIBITOR. | ||||||
Components | STROMELYSIN-1 | ||||||
Keywords | HYDROLASE / MIXED ALPHA BETA STRUCTURE / ZINC PROTEASE / INHIBITED | ||||||
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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / collagen catabolic process / extracellular matrix disassembly ...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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / regulation of cell migration / extracellular matrix / extracellular matrix organization / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / protein catabolic process / 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 / Resolution: 2.6 Å | ||||||
Authors | Almstead, N.G. / Bradley, R.S. / Pikul, S. / De, B. / Natchus, M.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1999 Title: Design, synthesis, and biological evaluation of potent thiazine- and thiazepine-based matrix metalloproteinase inhibitors. Authors: Almstead, N.G. / Bradley, R.S. / Pikul, S. / De, B. / Natchus, M.G. / Taiwo, Y.O. / Gu, F. / Williams, L.E. / Hynd, B.A. / Janusz, M.J. / Dunaway, C.M. / Mieling, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d5j.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d5j.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 1d5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d5j_validation.pdf.gz | 506.8 KB | Display | wwPDB validaton report |
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Full document | 1d5j_full_validation.pdf.gz | 527.8 KB | Display | |
Data in XML | 1d5j_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1d5j_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/1d5j ftp://data.pdbj.org/pub/pdb/validation_reports/d5/1d5j | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#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) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08254, stromelysin 1 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | #5: 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: 2.01 Å3/Da / Density % sol: 38.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 6000, NACL, MGCL2, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. all: 10092 / Num. obs: 9752 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 18.18 Å2 / Rmerge(I) obs: 0.184 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.468 / Num. unique all: 994 / % possible all: 99.1 |
Reflection shell | *PLUS % possible obs: 99.1 % |
-Processing
Software |
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Refinement | Resolution: 2.6→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 98.1 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.009 |