[English] 日本語
Yorodumi- PDB-6w0t: Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w0t | ||||||
---|---|---|---|---|---|---|---|
Title | Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments | ||||||
Components | Non-structural protein 3 | ||||||
Keywords | VIRAL PROTEIN / Chikungunya virus / nsP3 / Macrodomain / pyrimidone fragments | ||||||
Function / homology | Function and homology information polynucleotide 5'-phosphatase / : / 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 ...polynucleotide 5'-phosphatase / : / 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 / Transferases; Transferring one-carbon groups; Methyltransferases / host cell 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 Similarity search - Function | ||||||
Biological species | Chikungunya virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Wu, M. / Zhang, S. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Plos One / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6w0t.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6w0t.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 6w0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w0t_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6w0t_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 6w0t_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 6w0t_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/6w0t ftp://data.pdbj.org/pub/pdb/validation_reports/w0/6w0t | HTTPS FTP |
-Related structure data
Related structure data | 6vuqSC 6w7hC 6w8kC 6w8mC 6w8qC 6w8yC 6w8zC 6w91C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18518.877 Da / Num. of mol.: 4 / Fragment: residues 1334-1493 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus (strain 37997) / Strain: 37997 / Production host: Escherichia coli (E. coli) References: UniProt: Q5XXP4, UniProt: Q8JUX6*PLUS, ADP-ribose 1''-phosphate phosphatase #2: Chemical | ChemComp-S6Y / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→76.28 Å / Num. obs: 52180 / % possible obs: 98.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.514 / Num. unique obs: 3570 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VUQ Resolution: 1.95→76.01 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.465 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.165 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.06 Å2 / Biso mean: 47.018 Å2 / Biso min: 22.86 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→76.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|