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Yorodumi- PDB-3hy7: Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hy7 | ||||||
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Title | Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with Marimastat | ||||||
Components | A disintegrin and metalloproteinase with thrombospondin motifs 5 | ||||||
Keywords | HYDROLASE / alpha/beta structure / central five stranded beta-sheet / Cleavage on pair of basic residues / Disulfide bond / Extracellular matrix / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen | ||||||
Function / homology | Function and homology information Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / pulmonary valve morphogenesis / myoblast fusion / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / extracellular matrix binding / aortic valve morphogenesis / negative regulation of cold-induced thermogenesis / endocardial cushion morphogenesis / extracellular matrix disassembly ...Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / pulmonary valve morphogenesis / myoblast fusion / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / extracellular matrix binding / aortic valve morphogenesis / negative regulation of cold-induced thermogenesis / endocardial cushion morphogenesis / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / metallopeptidase activity / integrin binding / heparin binding / peptidase activity / collagen-containing extracellular matrix / endopeptidase activity / defense response to bacterium / endoplasmic reticulum lumen / proteolysis / extracellular space / zinc ion binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å | ||||||
Authors | Shieh, H.-S. / Williams, J.M. / Caspers, N. / Mathis, K.J. / Tortorella, M.D. / Tomasselli, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural and inhibition analysis reveals the mechanism of selectivity of a series of aggrecanase inhibitors Authors: Tortorella, M.D. / Tomasselli, A.G. / Mathis, K.J. / Schnute, M.E. / Woodard, S.S. / Munie, G. / Williams, J.M. / Caspers, N. / Wittwer, A.J. / Malfait, A.M. / Shieh, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hy7.cif.gz | 113.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hy7.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/3hy7 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/3hy7 | HTTPS FTP |
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-Related structure data
Related structure data | 3hy9C 3hygC 3b8zS S: Starting model for refinement C: citing same article (ref.) |
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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: 24436.645 Da / Num. of mol.: 2 / Fragment: Catalytic Domain (UNP residues 262 to 480) / Mutation: L282K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS-5, ADAMTS11, ADAMTS5, ADMP2 / Plasmid: PPHA79257 / Production host: Escherichia coli (E. coli) / Strain (production host): MON208 References: UniProt: Q9UNA0, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / #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: 1.86 Å3/Da / Density % sol: 33.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 3350, 200 mM ammonium acetate, 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 39500 / Num. obs: 38276 / % possible obs: 96.9 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3239 / Rsym value: 0.35 / % possible all: 83.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3B8Z Resolution: 1.69→26.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.511 / SU ML: 0.084 / Isotropic thermal model: Individual isotropic / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.128 / 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: 20.831 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→26.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.693→1.737 Å / Total num. of bins used: 20
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