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Yorodumi- PDB-6tvx: Human CD73 (ecto 5'-nucleotidase) in complex with PSB12676 (an AO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tvx | ||||||
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Title | Human CD73 (ecto 5'-nucleotidase) in complex with PSB12676 (an AOPCP derivative, compound 9 in paper) in the closed state | ||||||
Components | 5'-nucleotidase | ||||||
Keywords | HYDROLASE / nucleotide analog / eN / 5NT / complex | ||||||
Function / homology | Function and homology information thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process / GMP 5'-nucleotidase activity / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Nicotinate metabolism / Purine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / DNA metabolic process / leukocyte cell-cell adhesion / response to ATP / response to inorganic substance / calcium ion homeostasis / Purinergic signaling in leishmaniasis infection / ATP metabolic process / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Pippel, J. / Strater, N. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: 2-Substituted alpha , beta-Methylene-ADP Derivatives: Potent Competitive Ecto-5'-nucleotidase (CD73) Inhibitors with Variable Binding Modes. Authors: Bhattarai, S. / Pippel, J. / Scaletti, E. / Idris, R. / Freundlieb, M. / Rolshoven, G. / Renn, C. / Lee, S.Y. / Abdelrahman, A. / Zimmermann, H. / El-Tayeb, A. / Muller, C.E. / Strater, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tvx.cif.gz | 412.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tvx.ent.gz | 339.8 KB | Display | PDB format |
PDBx/mmJSON format | 6tvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/6tvx ftp://data.pdbj.org/pub/pdb/validation_reports/tv/6tvx | HTTPS FTP |
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-Related structure data
Related structure data | 6tveC 6tvgC 6tw0C 6twaC 6twfC 4h2iS 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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Unit cell |
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-Components
#1: Protein | Mass: 59260.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Production host: Escherichia coli (E. coli) / References: UniProt: P21589, 5'-nucleotidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NYW / [[( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Drop: 3 mg/ml CD73, 100 microM ZnCl2 and 1 mM of compound. Reservoir: 5-8 percent (w/v) polyethylene glycol 6000, 0.1 M NaMES pH 5.5. Cryo buffer: 25 percent PEG200, 0.1 M NaMES pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→47.7 Å / Num. obs: 19655 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 69.67 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.354 / Rpim(I) all: 0.149 / Rrim(I) all: 0.385 / Net I/σ(I): 5.7 / Num. measured all: 129595 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4h2i Resolution: 2.6→47.7 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.869 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.604 / SU Rfree Blow DPI: 0.289
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Displacement parameters | Biso max: 213.34 Å2 / Biso mean: 95.59 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→47.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 26
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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