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- PDB-6tvx: Human CD73 (ecto 5'-nucleotidase) in complex with PSB12676 (an AO... -
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Open data
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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 | ||||||
![]() | 5'-nucleotidase | ||||||
![]() | HYDROLASE / nucleotide analog / eN / 5NT / complex | ||||||
Function / homology | ![]() 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 / GMP 5'-nucleotidase activity ...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 / GMP 5'-nucleotidase activity / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / AMP catabolic process / Nicotinate metabolism / Purine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / leukocyte cell-cell adhesion / DNA metabolic process / response to ATP / : / 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 / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pippel, J. / Strater, N. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 412.2 KB | Display | ![]() |
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PDB format | ![]() | 339.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.5 KB | Display | ![]() |
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Full document | ![]() | 780.1 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tveC ![]() 6tvgC ![]() 6tw0C ![]() 6twaC ![]() 6twfC ![]() 4h2iS 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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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.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NYW / [[( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
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
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Refinement | Method to determine structure: ![]() 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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