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Yorodumi- PDB-8pie: Crystal structure of the human nucleoside diphosphate kinase B do... -
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-Basic information
Entry | Database: PDB / ID: 8pie | ||||||
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Title | Crystal structure of the human nucleoside diphosphate kinase B domain in complex with the product AT-8500 formed by catalysis of compound AT-9010 | ||||||
Components | Nucleoside diphosphate kinase B | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process ...regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / histidine kinase / ruffle / positive regulation of epithelial cell proliferation / cell periphery / integrin-mediated signaling pathway / GDP binding / lamellipodium / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / transcription coactivator activity / cell adhesion / Neutrophil degranulation / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Feracci, M. / Chazot, A. / Ferron, F. / Alvarez, K. / Canard, B. | ||||||
Funding support | France, 1items
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Citation | Journal: Plos Biol. / Year: 2024 Title: The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution. Authors: Chazot, A. / Zimberger, C. / Feracci, M. / Moussa, A. / Good, S. / Sommadossi, J.P. / Alvarez, K. / Ferron, F. / Canard, B. #1: Journal: Biorxiv / Year: 2024 Title: The activation chain of the broad-spectrum antiviral bemnifosbuvir at atomic resolution Authors: Chazot, A. / Zimberger, C. / Feracci, M. / Moussa, A. / Good, S. / Sommadossi, J.P. / Alvarez, K. / Ferron, F. / Canard, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pie.cif.gz | 380.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pie.ent.gz | 304.4 KB | Display | PDB format |
PDBx/mmJSON format | 8pie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pie_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8pie_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8pie_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 8pie_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/8pie ftp://data.pdbj.org/pub/pdb/validation_reports/pi/8pie | HTTPS FTP |
-Related structure data
Related structure data | 8ptsC 8pwkC 8qchC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.51093/xrd-00152 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 6 - 156 / Label seq-ID: 21 - 171
NCS ensembles :
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-Components
#1: Protein | Mass: 19547.240 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NME2, NM23B / Production host: Escherichia coli (E. coli) References: UniProt: P22392, nucleoside-diphosphate kinase, histidine kinase #2: Chemical | ChemComp-7QT / [( Mass: 459.218 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H16FN5O10P2 #3: Chemical | ChemComp-GOL / | #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: 2.12 Å3/Da / Density % sol: 41.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: mixing 1:1 ration with precipitant solution composed of: -50mM Tris-HCl pH8.4 -12% PEG3350 -16% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98010736891201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98010736891201 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.68 Å / Num. obs: 67263 / % possible obs: 98.89 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rpim(I) all: 0.0552 / Net I/σ(I): 8.61 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.57 / Num. unique obs: 6623 / CC1/2: 0.793 / Rpim(I) all: 0.3295 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.68 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.633 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.145 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.719 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→49.68 Å
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Refine LS restraints |
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