+Open data
-Basic information
Entry | Database: PDB / ID: 6tve | ||||||
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Title | Unliganded human CD73 (5'-nucleotidase) in the open state | ||||||
Components | 5'-nucleotidase | ||||||
Keywords | HYDROLASE / eN / e5NT / dizinc / ecto-nucleotidase | ||||||
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 / : / Purinergic signaling in leishmaniasis infection / calcium ion homeostasis / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å | ||||||
Authors | Scaletti, E. / 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 | 6tve.cif.gz | 411.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tve.ent.gz | 279 KB | Display | PDB format |
PDBx/mmJSON format | 6tve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tve_validation.pdf.gz | 457.2 KB | Display | wwPDB validaton report |
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Full document | 6tve_full_validation.pdf.gz | 458 KB | Display | |
Data in XML | 6tve_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 6tve_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/6tve ftp://data.pdbj.org/pub/pdb/validation_reports/tv/6tve | HTTPS FTP |
-Related structure data
Related structure data | 6tvgC 6tvxC 6tw0C 6twaC 6twfC 2h2gS 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
-Protein , 1 types, 1 molecules P
#1: Protein | Mass: 60464.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: construct 2.71 / 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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-Non-polymers , 5 types, 699 molecules
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-DMS / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 100 mM Tris pH 7.8, PEG6000, 100 mM Gly-Pro, 10 % DMSO. The Gly-Pro dipeptide was added as part of fragment screening experiment but did not bind to the protein. |
-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: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→32.84 Å / Num. obs: 267271 / % possible obs: 98.5 % / Redundancy: 6.56 % / Biso Wilson estimate: 8.91 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.05→1.09 Å / Redundancy: 5.93 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 12510 / CC1/2: 0.636 / Rrim(I) all: 0.858 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2h2g Resolution: 1.05→32.84 Å / SU ML: 0.0756 / Cross valid method: FREE R-VALUE / Phase error: 10.4204
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→32.84 Å
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Refine LS restraints |
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LS refinement shell |
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