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Yorodumi- PDB-6ye1: Human Ecto-5'-nucleotidase (CD73) in complex with the AMPCP deriv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ye1 | ||||||
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Title | Human Ecto-5'-nucleotidase (CD73) in complex with the AMPCP derivative A894 (compound 2n in publication) in the closed form (crystal form IV) | ||||||
Components | 5'-nucleotidase | ||||||
Keywords | HYDROLASE / competitive nucleotide 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 / 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 / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.66 Å | ||||||
Model details | The compound is a competitive non-nucleotide inhibitor binding to the active site | ||||||
Authors | Scaletti, E. / Strater, N. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of Potent and Selective Methylenephosphonic Acid CD73 Inhibitors. Authors: Sharif, E.U. / Kalisiak, J. / Lawson, K.V. / Miles, D.H. / Newcomb, E. / Lindsey, E.A. / Rosen, B.R. / Debien, L.P.P. / Chen, A. / Zhao, X. / Young, S.W. / Walker, N.P. / Strater, N. / ...Authors: Sharif, E.U. / Kalisiak, J. / Lawson, K.V. / Miles, D.H. / Newcomb, E. / Lindsey, E.A. / Rosen, B.R. / Debien, L.P.P. / Chen, A. / Zhao, X. / Young, S.W. / Walker, N.P. / Strater, N. / Scaletti, E.R. / Jin, L. / Xu, G. / Leleti, M.R. / Powers, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ye1.cif.gz | 432.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ye1.ent.gz | 356.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ye1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ye1_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ye1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ye1_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 6ye1_validation.cif.gz | 57.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/6ye1 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/6ye1 | HTTPS FTP |
-Related structure data
Related structure data | 6ye2C 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.: 2 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 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1mM of compound, 0.1 mM ZnCl2, 11-14% PEG6000, 100 mM sodium citrate pH 5.4-5.6, 15% glycerol for cryo PH range: 5.4-5.6 |
-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: Jun 23, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.66→46.52 Å / Num. obs: 34420 / % possible obs: 99.6 % / Redundancy: 6.531 % / Biso Wilson estimate: 45.71 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.253 / Rrim(I) all: 0.275 / Χ2: 0.949 / Net I/σ(I): 6.99 / Num. measured all: 224786 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.66→46.52 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.877 / SU R Cruickshank DPI: 2.594 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.355 / SU Rfree Cruickshank DPI: 0.354
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Displacement parameters | Biso max: 147.12 Å2 / Biso mean: 58.63 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.66→46.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | T11: 0.304 Å2 / T22: -0.304 Å2 / T33: -0.304 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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