[English] 日本語
Yorodumi- PDB-6yjm: Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yjm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with the Inhibitor GLPG1972 | ||||||
Components | A disintegrin and metalloproteinase with thrombospondin motifs 5 | ||||||
Keywords | HYDROLASE / zinc metalloproteinase / aggrecanase | ||||||
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 / extracellular matrix organization / metalloendopeptidase activity / integrin binding / metallopeptidase activity / heparin binding / peptidase activity / endopeptidase activity / collagen-containing extracellular matrix / 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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Goepfert, A. / Leonard, P. / Triballeau, N. / Fleury, D. / Mollat, P. / Lamers, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of GLPG1972/S201086, a Potent, Selective, and Orally Bioavailable ADAMTS-5 Inhibitor for the Treatment of Osteoarthritis. Authors: Brebion, F. / Gosmini, R. / Deprez, P. / Varin, M. / Peixoto, C. / Alvey, L. / Jary, H. / Bienvenu, N. / Triballeau, N. / Blanque, R. / Cottereaux, C. / Christophe, T. / Vandervoort, N. / ...Authors: Brebion, F. / Gosmini, R. / Deprez, P. / Varin, M. / Peixoto, C. / Alvey, L. / Jary, H. / Bienvenu, N. / Triballeau, N. / Blanque, R. / Cottereaux, C. / Christophe, T. / Vandervoort, N. / Mollat, P. / Touitou, R. / Leonard, P. / De Ceuninck, F. / Botez, I. / Monjardet, A. / van der Aar, E. / Amantini, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6yjm.cif.gz | 102 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6yjm.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 6yjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yjm_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6yjm_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6yjm_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 6yjm_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/6yjm ftp://data.pdbj.org/pub/pdb/validation_reports/yj/6yjm | HTTPS FTP |
-Related structure data
Related structure data | 3ljtS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24700.969 Da / Num. of mol.: 2 / Mutation: L282K Source method: isolated from a genetically manipulated source Details: The three last amino acids of the sequence (VPR) are part of an engineered Thrombin enzyme cleavage site. Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS5, ADAMTS11, ADMP2 / Production host: Homo sapiens (human) References: UniProt: Q9UNA0, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.85 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES pH 7.0, 300% v/v Jeffamine ED-2001 pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→18.5 Å / Num. obs: 15333 / % possible obs: 86.24 % / Redundancy: 5 % / Biso Wilson estimate: 16.796483553 Å2 / CC1/2: 0.948 / CC star: 0.986 / Net I/σ(I): 19.05 |
Reflection shell | Resolution: 2.25→2.33 Å / Mean I/σ(I) obs: 5.4 / Num. unique obs: 877 / CC1/2: 0.671 / CC star: 0.896 / % possible all: 51.02 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LJT Resolution: 2.25→18.47 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.862 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso mean: 18.366 Å2
| ||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.25→18.47 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
|