+Open data
-Basic information
Entry | Database: PDB / ID: 7jv8 | ||||||
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Title | Human CD73 (ecto 5'-nucleotidase) in complex with compound 35 | ||||||
Components | 5'-nucleotidase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / 5'-NUCLEOTIDASE / HYDROLASE / PHOSPHATASE / PROTEROS / PROTEROS BIOSTRUCTURES GMBH / HYDROLASE-HYDROLASE INHIBITOR 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 / : / 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 / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Gibbons, P. / Du, X. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Orally Bioavailable Small-Molecule CD73 Inhibitor (OP-5244) Reverses Immunosuppression through Blockade of Adenosine Production. Authors: Du, X. / Moore, J. / Blank, B.R. / Eksterowicz, J. / Sutimantanapi, D. / Yuen, N. / Metzger, T. / Chan, B. / Huang, T. / Chen, X. / Chen, Y. / Duong, F. / Kong, W. / Chang, J.H. / Sun, J. / ...Authors: Du, X. / Moore, J. / Blank, B.R. / Eksterowicz, J. / Sutimantanapi, D. / Yuen, N. / Metzger, T. / Chan, B. / Huang, T. / Chen, X. / Chen, Y. / Duong, F. / Kong, W. / Chang, J.H. / Sun, J. / Zavorotinskaya, T. / Ye, Q. / Junttila, M.R. / Ndubaku, C. / Friedman, L.S. / Fantin, V.R. / Sun, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jv8.cif.gz | 425.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jv8.ent.gz | 343 KB | Display | PDB format |
PDBx/mmJSON format | 7jv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jv8_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7jv8_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7jv8_validation.xml.gz | 74.8 KB | Display | |
Data in CIF | 7jv8_validation.cif.gz | 104.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/7jv8 ftp://data.pdbj.org/pub/pdb/validation_reports/jv/7jv8 | HTTPS FTP |
-Related structure data
Related structure data | 7jv9C 6tveS 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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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 58765.887 Da / Num. of mol.: 4 / Mutation: N53D, N333D, N403D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P21589, 5'-nucleotidase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-VPD / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.10M SPG (Succinic Acid, Sodium Dihydrogen Phosphate and Glycine) pH=4.00, 19.00 %w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→126.17 Å / Num. obs: 77008 / % possible obs: 94.7 % / Redundancy: 2.7 % / Rrim(I) all: 0.102 / Rsym value: 0.083 / Net I/σ(I): 11.15 |
Reflection shell | Resolution: 2.46→2.71 Å / Redundancy: 2.7 % / Num. unique obs: 19622 / Rrim(I) all: 0.534 / Rsym value: 0.439 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TVE Resolution: 2.46→126.17 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / SU B: 12.589 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.759 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 160.35 Å2 / Biso mean: 45.205 Å2 / Biso min: 14.13 Å2
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Refinement step | Cycle: final / Resolution: 2.46→126.17 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.02 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.46→2.524 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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