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- PDB-3hyg: Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hyg | ||||||
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Title | Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with an Amino-2-indanol compound | ||||||
![]() | A disintegrin and metalloproteinase with thrombospondin motifs 5 | ||||||
![]() | 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 | ![]() 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 / peptidase activity / heparin binding / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shieh, H.-S. / Williams, J.M. / Caspers, N. / Mathis, K.J. / Tortorella, M.D. / Tomasselli, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.4 KB | Display | ![]() |
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PDB format | ![]() | 86.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hy7C ![]() 3hy9C ![]() 3b8zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | dimer in the aymmetric unit |
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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.) ![]() ![]() ![]() References: UniProt: Q9UNA0, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.35 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 70408 / Num. obs: 70056 / % possible obs: 99.5 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 11.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 6795 / Rsym value: 0.259 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: protein code 3B8Z Resolution: 1.4→26.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 0.985 / SU ML: 0.041 / Isotropic thermal model: Individual isotropic / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / 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: 15.837 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→26.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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