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Yorodumi- PDB-7qgl: Human CD73 (ecto 5'-nucleotidase) in complex with MRS4602 (a 3-me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qgl | ||||||
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Title | Human CD73 (ecto 5'-nucleotidase) in complex with MRS4602 (a 3-methyl-CMPCP derivative, compound 21 in paper) in the open state | ||||||
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 / : / 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 / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Strater, N. | ||||||
Funding support | Germany, 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 | 7qgl.cif.gz | 238.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qgl.ent.gz | 186.1 KB | Display | PDB format |
PDBx/mmJSON format | 7qgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qgl_validation.pdf.gz | 763.8 KB | Display | wwPDB validaton report |
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Full document | 7qgl_full_validation.pdf.gz | 765.4 KB | Display | |
Data in XML | 7qgl_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 7qgl_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/7qgl ftp://data.pdbj.org/pub/pdb/validation_reports/qg/7qgl | HTTPS FTP |
-Related structure data
Related structure data | 7qgaC 7qgmC 7qgoC 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60363.316 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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-Non-polymers , 5 types, 660 molecules
#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-BW0 / [[( | #5: Chemical | ChemComp-1PE / #6: Water | ChemComp-HOH / | |
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-Details
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: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 10 mM MRS4602, 100 microM ZnCl2, 8 % PEG 6.000, 0.1 M MES pH 6.2, 20 % PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 16, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→21.63 Å / Num. obs: 91996 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.031 / Rrim(I) all: 0.065 / Net I/σ(I): 14.8 / Num. measured all: 362347 / Scaling rejects: 217 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6tve Resolution: 1.5→21.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.061 Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso max: 116.04 Å2 / Biso mean: 14.73 Å2 / Biso min: 4.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→21.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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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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