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- PDB-6w8m: Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w8m | ||||||
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Title | Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments | ||||||
![]() | Nonstructural polyprotein | ||||||
![]() | VIRAL PROTEIN / nsP3 / Macrodomain / pyrimidone fragments | ||||||
Function / homology | ![]() host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Zhang, S. / Garzan, A. / Pathak, A.K. / Augelli-Szafran, C.E. / Wu, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design. Authors: Zhang, S. / Garzan, A. / Haese, N. / Bostwick, R. / Martinez-Gzegozewska, Y. / Rasmussen, L. / Streblow, D.N. / Haise, M.T. / Pathak, A.K. / Augelli-Szafran, C.E. / Wu, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.2 KB | Display | ![]() |
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PDB format | ![]() | 110.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 40.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vuqC ![]() 6w0tC ![]() 6w7hC ![]() 6w8kC ![]() 6w8qC ![]() 6w8yC ![]() 6w8zC ![]() 6w91C ![]() 6uvwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18518.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-TJY / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 21-24% PEG 400, 0.1 M sodium citrate pH5.6, 10% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→76.17 Å / Num. obs: 72803 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.75→1.795 Å / Rmerge(I) obs: 0.547 / Num. unique obs: 5130 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6UVW Resolution: 1.75→76.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.941 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.116 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.95 Å2 / Biso mean: 38.392 Å2 / Biso min: 21.33 Å2
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Refinement step | Cycle: final / Resolution: 1.75→76.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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