[English] 日本語
Yorodumi- PDB-6xug: Human Ecto-5'-nucleotidase (CD73) in complex with A2410 (compound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xug | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human Ecto-5'-nucleotidase (CD73) in complex with A2410 (compound 53 in publication) in the closed form in crystal form IV | |||||||||
Components | 5'-nucleotidase | |||||||||
Keywords | HYDROLASE / non-nucleotide inhibitor / Arcus Biosciences | |||||||||
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: 2.09 Å | |||||||||
Model details | The compound is a competitive non-nucleotide inhibitor binding to the active site | |||||||||
Authors | Strater, N. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of Potent and Selective Non-Nucleotide Small Molecule Inhibitors of CD73. Authors: Beatty, J.W. / Lindsey, E.A. / Thomas-Tran, R. / Debien, L. / Mandal, D. / Jeffrey, J.L. / Tran, A.T. / Fournier, J. / Jacob, S.D. / Yan, X. / Drew, S.L. / Ginn, E. / Chen, A. / Pham, A.T. / ...Authors: Beatty, J.W. / Lindsey, E.A. / Thomas-Tran, R. / Debien, L. / Mandal, D. / Jeffrey, J.L. / Tran, A.T. / Fournier, J. / Jacob, S.D. / Yan, X. / Drew, S.L. / Ginn, E. / Chen, A. / Pham, A.T. / Zhao, S. / Jin, L. / Young, S.W. / Walker, N.P. / Leleti, M.R. / Moschutz, S. / Strater, N. / Powers, J.P. / Lawson, K.V. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6xug.cif.gz | 437 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6xug.ent.gz | 353.4 KB | Display | PDB format |
PDBx/mmJSON format | 6xug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xug_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6xug_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6xug_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 6xug_validation.cif.gz | 69.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/6xug ftp://data.pdbj.org/pub/pdb/validation_reports/xu/6xug | HTTPS FTP |
-Related structure data
Related structure data | 6xueC 6xuqC 4h2iS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59444.477 Da / Num. of mol.: 2 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 |
---|
-Non-polymers , 5 types, 855 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.11 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Reservoir: 9 % PEG 6000, 0.1 M MES pH 5.8. Drop: 1 micro-L crystallization buffer +1 micro-L of 3 mg/mL CD73 in 10 mM Tris pH 8.0, 10 micro-M ZnCl2; 200 micro-M NaH2PO4, 3 % DMSO, compound: ...Details: Reservoir: 9 % PEG 6000, 0.1 M MES pH 5.8. Drop: 1 micro-L crystallization buffer +1 micro-L of 3 mg/mL CD73 in 10 mM Tris pH 8.0, 10 micro-M ZnCl2; 200 micro-M NaH2PO4, 3 % DMSO, compound: saturated solution. Cryo: 20% PEG200 in crystallization drop |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.09→86.81 Å / Num. obs: 70479 / % possible obs: 99.7 % / Redundancy: 9.1 % / Biso Wilson estimate: 25.56 Å2 / Rpim(I) all: 0.091 / Rrim(I) all: 0.281 / Net I/σ(I): 5.3 / Num. measured all: 643925 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4H2I Resolution: 2.09→72.67 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.219 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.177
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.44 Å2 / Biso mean: 40.31 Å2 / Biso min: 3 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→72.67 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.09→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|