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Yorodumi- PDB-3ljt: Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ljt | ||||||
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Title | Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with an Amino-2-indanol compound | ||||||
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 / Protease / Secreted / 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 / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / 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: 1.6 Å | ||||||
Authors | Shieh, H.-S. / Williams, J.M. / Caspers, N. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Structure analysis reveals the flexibility of the ADAMTS-5 active site. Authors: Shieh, H.S. / Tomasselli, A.G. / Mathis, K.J. / Schnute, M.E. / Woodard, S.S. / Caspers, N. / Williams, J.M. / Kiefer, J.R. / Munie, G. / Wittwer, A. / Malfait, A.M. / Tortorella, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ljt.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ljt.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ljt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/3ljt ftp://data.pdbj.org/pub/pdb/validation_reports/lj/3ljt | HTTPS FTP |
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-Related structure data
Related structure data | 3ljzC 3b8zS 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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Unit cell |
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Details | Monomer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24105.213 Da / Num. of mol.: 1 / Fragment: Catalytic Domain / 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 |
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-Non-polymers , 5 types, 299 molecules
#2: Chemical | ChemComp-LA3 / ( | ||
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#3: Chemical | ChemComp-EDO / | ||
#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.02 % |
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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: 21-ID-G / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 20954 / Num. obs: 20120 / % possible obs: 96 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 11.94 Å2 / Rsym value: 0.073 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1542 / Rsym value: 0.356 / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3B8Z Resolution: 1.6→38.12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.622 / SU ML: 0.059 / Isotropic thermal model: Individual isotropic / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / 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: 10.354 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→38.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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