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Yorodumi- PDB-7qgm: Human CD73 (ecto 5'-nucleotidase) in complex with MRS4598 (a 3-me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qgm | ||||||
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Title | Human CD73 (ecto 5'-nucleotidase) in complex with MRS4598 (a 3-methyl-CMPCP derivative, compound 16 in paper) in the closed state (crystal form III) | ||||||
Components | 5'-nucleotidase | ||||||
Keywords | HYDROLASE / en / e5nt / ecto-nucleotidase / inhibitor | ||||||
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: 2.9 Å | ||||||
Authors | Strater, N. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Structure-Activity Relationship of 3-Methylcytidine-5'-alpha , beta-methylenediphosphates as CD73 Inhibitors. Authors: Scortichini, M. / Idris, R.M. / Moschutz, S. / Keim, A. / Salmaso, V. / Dobelmann, C. / Oliva, P. / Losenkova, K. / Irjala, H. / Vaittinen, S. / Sandholm, J. / Yegutkin, G.G. / Strater, N. / ...Authors: Scortichini, M. / Idris, R.M. / Moschutz, S. / Keim, A. / Salmaso, V. / Dobelmann, C. / Oliva, P. / Losenkova, K. / Irjala, H. / Vaittinen, S. / Sandholm, J. / Yegutkin, G.G. / Strater, N. / Junker, A. / Muller, C.E. / Jacobson, K.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qgm.cif.gz | 307.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qgm.ent.gz | 255.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/7qgm ftp://data.pdbj.org/pub/pdb/validation_reports/qg/7qgm | HTTPS FTP |
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-Related structure data
Related structure data | 7qgaC 7qglC 7qgoC 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: 62277.922 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: Homo sapiens (human) / References: UniProt: P21589, 5'-nucleotidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-BOI / [[( | 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: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 10 mM MRS4598, 10 microM ZnCl2, 10 % PEG 3.350, 0.1 M BisTris pH 5.6, 10 mM MRS4598, 20 % PEG200 |
-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: 0.9184 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→48.05 Å / Num. obs: 14569 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 89.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.059 / Rrim(I) all: 0.206 / Net I/σ(I): 8.9 / Num. measured all: 175782 / Scaling rejects: 10 | ||||||||||||||||||||||||||||||
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: 2.9→47.98 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 198.24 Å2 / Biso mean: 109.3644 Å2 / Biso min: 60.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→47.98 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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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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