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Yorodumi- PDB-5cqz: Human cytosolic 5'-nucleotidase II in complex with 3-(3-Imidazol-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cqz | ||||||
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Title | Human cytosolic 5'-nucleotidase II in complex with 3-(3-Imidazol-1-ylphenyl)-N-(9H-purin-6-yl)benzamide | ||||||
Components | Cytosolic purine 5'-nucleotidase | ||||||
Keywords | HYDROLASE / HIGH KM 5-PRIME NUCLEOTIDASE / CN-II / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / HYDROLASE-HYDROLASE EFFECTOR COMPLEX | ||||||
Function / homology | Function and homology information nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Ribavirin ADME / IMP metabolic process / IMP catabolic process / Purine catabolism / allantoin metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Preeti, P. / Aghajari, N. | ||||||
Funding support | France, 1items
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Citation | Journal: J.Med.Chem. / Year: 2015 Title: Identification of Noncompetitive Inhibitors of Cytosolic 5'-Nucleotidase II Using a Fragment-Based Approach. Authors: Marton, Z. / Guillon, R. / Krimm, I. / Rahimova, R. / Egron, D. / Jordheim, L.P. / Aghajari, N. / Dumontet, C. / Perigaud, C. / Lionne, C. / Peyrottes, S. / Chaloin, L. #1: Journal: Biochem. Pharmacol. / Year: 2013 Title: Identification and characterization of inhibitors of cytoplasmic 5'-nucleotidase cN-II issued from virtual screening. Authors: Jordheim, L.P. / Marton, Z. / Rhimi, M. / Cros-Perrial, E. / Lionne, C. / Peyrottes, S. / Dumontet, C. / Aghajari, N. / Chaloin, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cqz.cif.gz | 205.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cqz.ent.gz | 161.8 KB | Display | PDB format |
PDBx/mmJSON format | 5cqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cqz_validation.pdf.gz | 491.2 KB | Display | wwPDB validaton report |
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Full document | 5cqz_full_validation.pdf.gz | 503.6 KB | Display | |
Data in XML | 5cqz_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 5cqz_validation.cif.gz | 48.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/5cqz ftp://data.pdbj.org/pub/pdb/validation_reports/cq/5cqz | HTTPS FTP |
-Related 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, 2 molecules AB
#1: Protein | Mass: 64088.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Plasmid: P28A-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 / References: UniProt: P49902, 5'-nucleotidase |
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-Non-polymers , 5 types, 101 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: MgSO4, Tris and ligand |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.97872 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50.9 Å / Num. obs: 30987 / % possible obs: 98.1 % / Redundancy: 3.3 % / Net I/σ(I): 10.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→19.882 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.91 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.882 Å
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Refine LS restraints |
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LS refinement shell |
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