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Yorodumi- PDB-6fir: Human cytosolic 5'-nucleotidase II soaked with 5mM3-Phenyl-N-(9H-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fir | |||||||||
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Title | Human cytosolic 5'-nucleotidase II soaked with 5mM3-Phenyl-N-(9H-purin-6-yl)benzamide | |||||||||
Components | Cytosolic purine 5'-nucleotidase | |||||||||
Keywords | HYDROLASE | |||||||||
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: 2.5 Å | |||||||||
Authors | Aghajari, N. / Preeti, P. | |||||||||
Funding support | France, 2items
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Citation | Journal: Eur J Med Chem / Year: 2019 Title: Lead optimization and biological evaluation of fragment-based cN-II inhibitors. Authors: Guillon, R. / Rahimova, R. / Egron, D. / Rouanet, S. / Dumontet, C. / Aghajari, N. / Jordheim, L.P. / Chaloin, L. / Peyrottes, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fir.cif.gz | 212.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fir.ent.gz | 168.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fir_validation.pdf.gz | 454.8 KB | Display | wwPDB validaton report |
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Full document | 6fir_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 6fir_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 6fir_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/6fir ftp://data.pdbj.org/pub/pdb/validation_reports/fi/6fir | HTTPS FTP |
-Related structure data
Related structure data | 6fisC 6fiuC 6fiwC 6fxhC 2j2cS 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: 64088.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE CONSTRUCT CONTAINS RESIDUES 1-536 OUT OF THE 561 AMINO ACIDS OF THE ENZYME. MOREOVER AN N-TERMINAL HISTAG (MGSSHHHHHHSSGLVPRGS) IS PRESENT. A NUMBER OF RESIDUES ARE NOT VISIBLE IN THE ELECTRON DENSITY 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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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: MGSO4, TRIS AND LIGAND, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 25195 / % possible obs: 94.4 % / Redundancy: 4.5 % / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J2C Resolution: 2.5→49 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 45.6231 Å / Origin y: -25.0075 Å / Origin z: -19.1953 Å
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Refinement TLS group | Selection details: all |